An extended novel approach of river health analysis using nonmetric scaling ordination of fish ecological entities and functional identity indices.

As river ecosystems continue to face environmental pressures, it is crucial to develop and apply new biologically relevant statistical tools to support river health assessments. This study aimed to test the potential significance of nonmetric ordination scores and multidimensional functional indices of fish communities for analyzing river ecological health linked to variations in environmental factors. We conducted a nonmetric multidimensional scaling (NMDS) to derive ordination scores based on twenty fish ecological entities (FEs) that we newly defined, along with their relative abundance (RA). These FEs were determined through a unique combination of trophic, habitat, and tolerance guilds. Additionally, we calculated the functional diversity and identity (F-Ide) indices using the RA-weighted distances between FEs defined by the guild identities in a multidimensional space. The results showed that these novel analyses were helpful in assessing river ecological health and spatial changes in the environment. The dominant F-Ide in each community was largely responsible for the variation of river health scores, driven by the combined impact of chemical water quality, alterations in substrate composition, land use changes, and the gradient of elevation. These environmental factors significantly influenced the site scores in the first axis of NMDS, F-Ide indices, and river health scores. Therefore, our study highlights the practical value of utilizing nonmetric scaling ordination scores of FEs and F-Ide indices as tools for evaluating the health of river ecosystems. By elucidating fish community variance, these tools can aid in determining the extent of river health degradation attributable to environmental stressors, including chemical water pollution and changes in substrate resulting from changes in land use and at different elevations.

Spatial and Temporal Dynamics of Prokaryotic and Viral Community Assemblages in a Lotic System (Manatee Springs, Florida).

Flow from high-magnitude springs fed by the Floridan aquifer system contributes hundreds of liters of water per second to rivers, creating unique lotic systems. Despite their importance as freshwater sources and their contributions to the state's major rivers, little is known about the composition and spatiotemporal variability of prokaryotic and viral communities of these spring systems or their influence on downstream river sites. At four time points throughout a year, we determined the abundance and diversity of prokaryotic and viral communities at three sites within the first-magnitude Manatee Springs system (the spring head where water emerges from the aquifer, a mixed region where the spring run ends, and a downstream site in the Suwannee River). The abundance of prokaryotes and virus-like particles increased 100-fold from the spring head to the river and few members from the head communities persisted in the river at low abundance, suggesting the springs play a minor role in seeding downstream communities. Prokaryotic and viral communities within Manatee Springs clustered by site, with seasonal variability likely driven by flow. As water flowed through the system, microbial community composition was affected by changes in physiochemical parameters and community coalescence. Evidence of species sorting and mass effects could be seen in the assemblages. Greater temporal fluctuations were observed in prokaryotic and viral community composition with increasing distance from the spring outflow, reflecting the relative stability of the groundwater environment, and comparisons to springs from prior work reaffirmed that distinct first-magnitude springs support unique communities. IMPORTANCE Prokaryotic and viral communities are central to food webs and biogeochemical processes in aquatic environments, where they help maintain ecosystem health. The Floridan aquifer system (FAS), which is the primary drinking water source for millions of people in the southeastern United States, contributes large amounts of freshwater to major river systems in Florida through its springs. However, there is a paucity of information regarding the spatiotemporal dynamics of microbial communities in these essential flowing freshwater systems. This work explored the prokaryotic and viral communities in a first-magnitude spring system fed by the FAS that discharges millions of liters of water per day into the Suwannee River. This study examined microbial community composition through space and time as well as the environmental parameters and metacommunity assembly mechanisms that shape these communities, providing a foundational understanding for monitoring future changes.

Fish size spectra are affected by nutrient concentration and relative abundance of non-native species across streams of the NE Iberian Peninsula.

Aquatic ecosystems are strongly body-size structured with a decline of numerical abundance with increasing body size (hereafter, the size spectrum). Marine and lake fish studies have reported consistent variations of size spectra in relation to environmental conditions and biotic composition, but little is known about stream fishes. Accordingly, in this study we test several hypotheses about the effects of local water conditions, biotic introductions and cumulative pressures (measured as the IMPRESS index) on the fish size-spectrum slope (that is, the linear rate of decline of fish abundance as body size increase in a log-log scale) and the size-spectrum intercept (commonly used as proxy for carrying capacity) among 118 local fish assemblages in streams of the NE Iberian Peninsula. To our knowledge, this is the first time that an extensive river fish dataset is used in a dendritic network to cover systematic changes of size-spectrum parameters. We find that the slope and intercept of the fish size spectrum are negatively correlated with nutrient concentration (mainly total phosphorus), with a greater relative abundance of small fishes but a decline of overall carrying capacity. Moreover, fish assemblages with greater relative abundance of non-native species have flatter size-spectrum slopes. In contrast, the IMPRESS index and climate-related variables are poor predictors of the shape of the fish size spectra. This study contributes to better understanding of the main factors structuring fish assemblages in lotic environments of the Iberian Peninsula. We encourage more research on this line to further explore the use of fish size structure to evaluate the ecological health of riverine ecosystems.

Assessment of potential reference sites for evaluating the ecological status of subtropical and temperate Brazilian lotic systems using the epilithic diatom community.

This research aimed at determining reference sites in southern Brazilian lotic systems, using the Water Quality Trophic Index (WQTI), based on epilithic diatom communities. Within the period of 2012 and 2016, 140 epilithic diatom samples from seven sampling sites within the spring area of the Andreas Stream Hydrographic Basin, Vera Cruz County, RS, Brazil, were analyzed quarterly. Similarly, from 2012 and 2014, water samples in these sampling sites were collected for determination of physicochemical and microbiological parameters, such as water temperature, pH, turbidity, dissolved oxygen, biochemical oxygen demand, nitrate, phosphate, total dissolved solids, and fecal coliforms. The results indicated the occurrence of two diatom samples groups with significant differences (p < 0.05). Group 1 (sampling sites P1, P4, and P5) was classified in the oligotrophic category with an average WQTI of 1.3 ± 0.2, while group 2 (sampling sites P2, P3, P6, and P7) was classified in the ß-mesotrophic category with an average value of 2.0 ± 0.4). Achnanthidium minutissimum and Platessa hustedtii the dominant species were classified as oligotrophic taxa. Thus, we proposed the upper limit of the first interval of the WQTI score scale, equal to 1.5, as a reference value to differentiate the limits between the "high" and "good" ecological status to determine "reference sites" for subtropical and temperate Brazilian aquatic systems. The physical, chemical, and microbiological water quality evaluation gives support to this proposal, as far as the results indicated a significant improvement in the water quality, classifying sampling sites P1, P4, and P5 as having good quality appropriate for multiple uses.

Downstream transport processes modulate the effects of environmental heterogeneity on riverine phytoplankton.

Environmental heterogeneity (EH) in space and time promotes niche-partition, which leads to high variation in biological communities, such as in algae. In streams, EH is highly related to the intensity of the water flow and may lead to community variation mainly during the low flow conditions. Despite the wide knowledge on the responses of phytoplankton communities to EH in lentic and semi-lentic systems, studies of riverine phytoplankton community variation are still scarce. Here, we first investigated the relationship between phytoplankton community variation and EH in different courses of the river and between seasons. We expected that under low or intermediate flow conditions, there is a positive correlation between community variation and EH. Alternatively, we did not expect any relationship between EH and community variation under high flow condition because stronger downstream transport would mask environmental filtering. We sampled nine sites monthly (May 2012 to April 2013) in a tropical river of Brazilian Southeast. We calculated EH from abiotic data whereas for community variation, here community distinctiveness (CD), we used Sorensen (CDSor) and Bray-Curtis (CDBray) dissimilarities. Differences in EH, CDSor and CDBray were tested at between-season and among-course levels. We found lower distinctiveness during the dry season when EH was the highest. Contrastingly, phytoplankton CD was the highest even when EH was low during the wet season. We found that this pattern raised from the increasing in individuals dispersal during the wet season, promoting mass effects. Finally, our results thus reject the first hypothesis and show a negative relationship between EH and distinctiveness. However, results support our alternative hypothesis and show that during the wet season, distinctiveness is not driven by EH. These results provide new insights into how EH drives community variation, being useful for both basic research about riverine algal communities and biomonitoring programs using phytoplankton communities as bioindicators.

Assessing the effects of water quality on leaf morphoanatomy, ultrastructure and photosynthetic pigment content of Salvinia auriculata Aubl. (Salviniaceae).

The objective of this study is to evaluate the effects of physical-chemical and biological variables of the water of the Capibaribe River (state of Pernambuco, Brazil) on leaf anatomy, including ultrastructure and photosynthetic pigment of Salvinia auriculata. Specimens of S. auriculata collected in the Gurjaú River, an area with a low pollution degree, were acclimatized in Hoagland's solution and then subjected to three water samples of the Capibaribe River with different levels of pollution. Twenty-one physical-chemical and biological variables were analyzed according to the Standard Methods for the Examination of Water and Wastewater. The results showed that the samples of the Capibaribe River presented nine parameters that did not comply with the current Brazilian legislation. After 15 days of bioassay, S. auriculata presented variations in mesophyll and cuticle thickness, changes in trichome morphology and accumulation of phenolic compounds. No significant differences were observed for photosynthetic pigment content and leaf length of S. auriculata. Multivariate analyses (PCA and Cluster) showed that the point in the Capibaribe River with the highest number of variables that do not comply with the current legislation was responsible for major structural and chemical changes observed in S. auriculata.

Water quality assessment of a neotropical pampean lowland stream using a phytoplankton functional trait approach.

The aim of this study was to test whether the water quality phytoplankton assemblage index adapted for rivers (Qr index) is useful to characterize the water quality of a neotropical stream. We were interested also in inferring the main pollutants through a phytoplankton functional trait characterization and assessing the phytoplankton groups which may influence the Qr index final estimations. Monthly sampling of environmental variables and phytoplankton were done in three sites (S1, S2, and S3). Phytoplankton was classified according to Reynolds Functional Groups (RFG) and water quality estimation was performed using the Qr index. Principal coordinates (PCO) and PERMANOVA were applied to identify the main pollutants through the RFG. RFG linkage to Qr values was assessed by general linear models (GLM). "Moderate" water quality was found in S1 the whole year, in all sampling stations during the winter, and in summer-autumn in S2. "Regular" water quality was found in S3 during the summer-autumn, and S2-S3 during the spring. S1 and S2 showed eutrophic, standing, or mix waters whereas S3 had high organic matter content and eutrophic conditions. Despite some RFG (X1 and MP) being linked to high Qr values and some other (M, S1 and Z) to low, their dominance did not influence water quality estimation performed by the Qr. We conclude that the Qr index was useful for assessing the water quality. Though RFG were valuable for inferring eutrophication, organic pollution, and mixing, but their dominance does not necessarily have a direct effect on the final Qr estimation.

Ecological drivers of alpha and beta diversity of freshwater invertebrates in arid and semiarid Patagonia (Argentina).

Freshwater biodiversity is showing a global decline in relation to environmental change and there is an urgent need to quantify different facets of biodiversity to assess the conservation value of freshwater ecosystems. Identifying the ecological drivers of arid and semiarid Patagonian waterbodies is a critical requirement for planning action to conserve these still poorly understood habitats. We tested the responses of alpha and beta diversity of invertebrates (presence-absence, abundance, and biomass) to local, landscape, and climatic features, in 45 Patagonian freshwater bodies classified in three groups: isolated ponds, connected ponds, and lotic systems. We first compared the invertebrate community compositions of the different waterbodies. Secondly, using a co-inertia analysis we assessed the relative roles of local, landscape and climatic factors in driving variation in assemblage composition. Finally, we compared different facets of beta diversity and modelled their responses to environmental variables (predictors), by generalized dissimilarity modelling (GDM). Unexpectedly, lotic systems with a total of 109 taxa, were richer than lentic ones, but isolated ponds contributed most to beta diversity and supported more unique and proportionally more endemic species. Alpha and beta diversity were mainly driven by local features and secondly by climatic descriptors. However, these patterns shifted according to different community composition measures. Collectively, our results suggest that isolated ponds have a higher biodiversity value and would be more vulnerable than connected ponds and lotic systems to environmental changes. However, all waterbody types contributed to gamma biodiversity, reinforcing the importance of conserving a diversity of freshwater ecosystems in any landscape and particularly in arid and semiarid Patagonia. Our findings are a first step to resolving and quantifying the amount of changes occurring in Patagonian waterbodies, and are a prerequisite for predicting changes in species distributions in the face of global change.

The Zygoptera/Anisoptera Ratio (Insecta: Odonata): a New Tool for Habitat Alterations Assessment in Amazonian Streams.

The accumulation of scientific knowledge is far outstripped by the rate of environmental disturbance from human activities in aquatic habitats. This highlights the need to develop effective proxy measures of aquatic biodiversity that can demonstrate changes in communities associated with human activities. We evaluated whether the relative abundance and species richness of Anisoptera and Zygoptera can be used as a tool to measure environmental impacts on Amazonian streams. Adult of Anisoptera and Zygoptera were sampled in 50 Amazonian streams, in the municipality of Paragominas (Pará state), Brazil, using an entomological handnet. The physical features of each stream were evaluated using an index of environmental integrity (HII). We collected a total of 1769 Odonata specimens, representing 97 species (56 were Zygoptera and 41 were Anisoptera). Habitat modification resulted in an inversion in the proportional abundance and species richness of Anisoptera and Zygoptera, where Zygoptera diversity decreased with the loss of habitat integrity, whereas Anisoptera diversity increased with habitat disturbance. A decline of 0.1 in the habitat integrity index score resulted in an increase of approximately 13 individuals and 11 species of Anisoptera, with the exact opposite effect observed for the Zygoptera. In summary, the Odonata proved to be a useful model for the assessment of Amazonian streams, with sites where more than 54% of the Odonata species were Zygoptera being classified as preserved, and those dominated by Anisoptera species (> 59%) being considered degraded. This approach has clear applications for environmental impact assessments, as it reduces the influence of sampling effort and collector experience on assessment outcomes, and does not rely upon specialist knowledge, given that members of the two suborders are easily distinguished from one and other in the field.

An analytical framework for estimating aquatic species density from environmental DNA.

Environmental DNA (eDNA) analysis of water samples is on the brink of becoming a standard monitoring method for aquatic species. This method has improved detection rates over conventional survey methods and thus has demonstrated effectiveness for estimation of site occupancy and species distribution. The frontier of eDNA applications, however, is to infer species density. Building upon previous studies, we present and assess a modeling approach that aims at inferring animal density from eDNA. The modeling combines eDNA and animal count data from a subset of sites to estimate species density (and associated uncertainties) at other sites where only eDNA data are available. As a proof of concept, we first perform a cross-validation study using experimental data on carp in mesocosms. In these data, fish densities are known without error, which allows us to test the performance of the method with known data. We then evaluate the model using field data from a study on a stream salamander species to assess the potential of this method to work in natural settings, where density can never be known with absolute certainty. Two alternative distributions (Normal and Negative Binomial) to model variability in eDNA concentration data are assessed. Assessment based on the proof of concept data (carp) revealed that the Negative Binomial model provided much more accurate estimates than the model based on a Normal distribution, likely because eDNA data tend to be overdispersed. Greater imprecision was found when we applied the method to the field data, but the Negative Binomial model still provided useful density estimates. We call for further model development in this direction, as well as further research targeted at sampling design optimization. It will be important to assess these approaches on a broad range of study systems.

Pesticide mixtures in streams of several European countries and the USA.

Given the multitude of pesticides used in agriculture, adjacent streams are typically exposed to pesticide mixtures. Previous studies analysed the ecological risks of a few pesticide mixtures or were limited to an individual region or crop, whereas a large scale analysis of pesticide mixtures is missing. We analysed routine monitoring data from Germany, France, the Netherlands and the USA comprising a total of 4532 sites and 56,084 sampling occasions with the aim to identify the most frequently detected pesticides, their metabolites and mixtures. The most frequently detected compounds were dominated by herbicides and their metabolites. Mixtures mostly comprised of two up to five compounds, whereas mixtures in the USA and France had clearly less compounds than those of Germany and the Netherlands. The number of detected pesticides and thereby the size of mixtures is positively correlated to the number of measured pesticides (r=0.57). In contrast, a low relationship was found to the ratio of agricultural areas within the catchment (r=0.17), and no relationship was found to the size of the catchment (r=0.06). Overall, our study provides priority mixtures for different countries that may be used for future ecotoxicological studies to improve risk assessment for stream ecosystems.

Surface coal mining influences on macroinvertebrate assemblages in streams of the Canadian Rocky Mountains.

To determine the region-specific impacts of surface coal mines on macroinvertebrate community health, chemical and physical stream characteristics and macroinvertebrate family and community metrics were measured in surface coal mine-affected and reference streams in the Canadian Rocky Mountains. Water chemistry was significantly altered in mine-affected streams, which had elevated conductivity, alkalinity, and selenium and ion concentrations compared with reference conditions. Multivariate redundancy analysis (RDA) indicated alterations in macroinvertebrate communities downstream of mine sites. In RDA ordination, Ephemeroptera family densities, family richness, Ephemeroptera, Plecoptera, Trichoptera (EPT) richness, and % Ephemeroptera declined, whereas densities of Capniidae stoneflies increased along environmental gradients defined by variables associated with mine influence including waterborne Se concentration, alkalinity, substrate embeddedness, and interstitial material size. Shifts in macroinvertebrate assemblages may have been the result of multiple region-specific stressors related to mining influences including selenium toxicity, ionic toxicity, or stream substrate modifications.

Epiphytic Eunotia (Bacillariophyceae) on Podostemum from Santa Catarina, southern Brazil, including new observations on morphology and taxonomy of some rare recorded species / Eunotia (Bacillariophyceae) epífitas sobrePodostemum em Santa Catarina, sul do Brasil, incluindo novas observações sobre a morfologia e taxonomia de espécies raramente registradas

Eunotia is a highly diverse diatom genus in the Neotropics. Considerable morphological variability of the valve showed in several species of the genus resulted in a quite confused taxonomy. Twelve Eunotiataxa attached to Podostemum spp. were investigated using the light microscopy (LM). Additionally, scanning electron microscopy (SEM) was used in order to investigate the fine morphology of most abundant taxa. Samples were collected from four rivers from the State of Santa Catarina between March 2009 and July 2010. The freshwater diatom flora from this south Brazilian state is poorly known in relation to its neighboring states. Eunotia biseriatoides has intermediate features betweenEunotia and Perinotia, and the circumscription of these genera is discussed here. Eunotia odebrechtiana is very similar in morphology to E. biseriatoides, and the synonymy is proposed, as well as the transfer of the variety E. odebrechtiana var.essequiboensis to the species E. biseriatoides. The fine structure of E. epithemioides is showed for the first time in SEM, revealing the unusual position of the rimoportula in this genus. A new variety, E. pseudosudetica var. rotundata var. nov., was proposed and compared with the typical one. Except by E. veneris, all other eleven taxa presented here are new records for the State of Santa Catarina, Brazil.

Eunotia é um gênero de diatomáceas altamente diverso na região neotropical. A considerável variabilidade morfológica encontrada nas valvas de várias espécies deste gênero resultam em uma taxonomia muito confusa. Neste estudo, 12 táxons de Eunotia aderidos a Podostemumspp. foram investigados usando microscopia óptica (MO). Adicionalmente, microscopia eletrônica de varredura (MEV) foi utilizada para investigar a morfologia ultraestrutural de táxons mais abundantes. Amostras foram coletadas em quatro rios do Estado de Santa Catarina entre março de 2009 e julho de 2010. A diatomoflórula deste estado é pobremente conhecida em relação aos estados vizinhos no sul do país. Eunotia biseriatoides é um taxon com características intermediárias entre Eunotia e Perinotiae a circunscrição destes gêneros é discutida aqui.Eunotia odebrechtiana é muito similar morfologicamente a E. biseriatoides e a sinonimização é proposta, bem como a transferência da variedade E. odebrechtianavar. essequiboensis è espécie E. biseriatoides. A ultraestrutura de E. epithemioides é apresentada pela primeira vez em MEV, revelando a posição atípica da rimoportula dentro deste gênero. Uma nova variedade, E. pseudosudetica var.rotundata var. nov., foi proposta e comparada com a variedade típica. Com exceção de E. veneris, todos os outros 11 táxons apresentados aqui são novos registros para Santa Catarina.

Second floor, please: the fish fauna of floating litter banks in Amazonian streams and rivers

Floating litter banks are an ephemeral habitat consisting of branches, twigs, flowers, seeds, and fruits that are trapped on the stream water surface by a variety of retention mechanisms. These heterogeneous materials form a deep layer of dead plant matter that is colonized by a variety of organisms, including fish that forage on the aquatic macroinvertebrates found in this unique habitat. In this study, we aimed to characterize which fish species occupy the floating litter banks and their trophic characteristics, as well as determine if fish assemblage composition and species richness can be predicted by the size of the floating litter banks. Fish sampling was conducted in five rivers located in the Amazon basin. Of the 31 floating litter banks sampled that contained fish, 455 individuals were recorded and were distributed within 40 species, 15 families and five orders. Siluriformes were the most representative order among the samples and contained the largest number of families and species. The fish fauna sampled was mainly composed of carnivorous species that are typically found in submerged litter banks of Amazonian streams. The fish assemblage composition in the kinon can be predicted by the volume of the floating litter banks using both presence/absence and abundance data, but not its species richness. In conclusion, kinon banks harbor a rich fish assemblage that utilizes this habitat for shelter and feeding, and may function as a refuge for the fishes during the peak of the flooding season.

Bancos de folhiço flutuantes são habitats efêmeros constituídos de troncos e galhos de árvores, flores, sementes e frutos retidos por uma variedade de mecanismos. Estes materiais formam uma camada espessa de matéria vegetal morta, que é colonizada por diferentes organismos, incluindo peixes que se alimentam de macroinvertebrados aquáticos presentes neste habitat. Nosso objetivo foi caracterizar as espécies e características tróficas dos peixes que ocupam esses bancos de folhiço flutuantes, bem como determinar se a composição da assembleia de peixes e a riqueza de espécies podem ser previstas pelo tamanho dos bancos. A amostragem dos peixes foi realizada em cinco rios da bacia amazônica. Dos 31 bancos de folhiço flutuantes amostrados que continham peixes, foram registrados 455 indivíduos distribuídos em 40 espécies, 15 famílias e cinco ordens. Siluriformes foi a ordem mais representativa, com o maior número de espécies e famílias. A fauna de peixes coletados foi composta principalmente por espécies carnívoras, que geralmente são encontrados em bancos de folhiço submersos de igarapés amazônicos. A composição das assembleias de peixes do 'kinon' pode ser prevista pelo volume desses bancos de liteira flutuante, tanto utilizando dados de presença/ausência quanto de abundância, mas não de riqueza de espécies. Em conclusão, os bancos de folhiço flutuante abrigam uma rica assembleia de peixes, que utilizam esse habitat como local de abrigo e de alimentação, e podem funcionar como refúgio para a ictiofauna dos bancos de folhiço submerso durante a estação chuvosa.

Diatomeas periftticas en diferentes tramos de ds sistemas lóticos de alta monttaña (páramo de santurbán, norte de santander, Colombia) y su relación con las variables ambientales / Perifitic Diatoms in Different Reach of Two Lotic Systems in High Mountain (Páramo de Santurbán, Norte de Santander, Colombia) and Their Relation with Environmental Variables

En dos sistemas lóticos del páramo de Santurbán, durante lluvia y sequía, se seleccionaron tres tramos de muestreo: nacimiento, zona media y río, evaluando en cada tramo la influencia de las variables ambientales en la estructura del ensamblaje de diatomeas perifíticas. Un nálisis de componentes principales evaluó la variación ambiental y mediante una matriz de correlaciones se estableció la importancia de los factores ambientales en las especies registradas. La conductividad, el potencial redox, el pH y el caudal fueron factores determinantes de la variación ambiental y de las diferencias en la estructura del ensamblaje; el género Eunotia es tolerante a pH ácido, y la polución orgánica favoreció el desarrollo de los géneros Nitzschia y Navícula. Seis especies reportaron una abundancia significativa: Navicula tantula, Achnanthidium minutissimum, Achnanthidium lanceolatum, Gomphonema parvulum, Navicula cryptocephala y Gomphonema lagenula. Los tramos de los ríos presentaron valores altos de caudal y conductividad, que influyeron en la baja diversidad de estas zonas mientras que los valores bajos de caudal y la ausencia de condiciones químicas extremas en las zonas medias explicaron la mayor diversidad y la similitud del ensamblaje entre estas zonas. El ensamblaje no registró variación estacional significativa, presentando mayores diferencias entre los tramos que entre períodos de muestreo, indicando que las diatomeas perifíticas fueron afectadas principalmente por diferencias en el hábitat entre los tramos y enfatizando la importancia de las condiciones ambientales en los sistemas acuáticos tropicales de alta montaña sobre la composición y abundancia de diatomeas perifíticas.

Three sample zones: the headwater zone, the mid flow zone and the stream zone were selected in two lotic system of the Páramo de Santurbán, during rainy and dry season. In each zone the influence of physical, chemical and hydrological variables on the structure of the benthic diatom assemblage were evaluated. A component principal analysis evaluated the environmental variation. A correlation matrix established the importance of the environmental factors in the registered species. Conductivity, redox potential, pH, and flow, were determinant factors on the environmental variation and on the assemblage structure differences between the zones. Acidity allowed the high occurrence of Eunotia species, and organic pollution allowed the abundance of Nitzchia and Navicula species. Six species were abundant: Navicula tantula, Achnanthidium minutissimum, Achnanthidium lanceolatum, Gomphonema parvulum, Navicula cryptocephala and Gomphonema lagenula. The stream zones registered high values of flow and conductivity, which were related with their lower diversity. Low flow and little stress condition on the mid flow zones were correlated with the highest values of diversity and with the similarity found in the dominant species between these zones in the two systems. The assemblage did not register seasonal variation; dissimilarity of diatom assemblages was larger among samples from different reach, compared with samples of different periods of the same reach, indicating that benthic diatom assemblages in the Páramo de Santurbán were mainly affected by habitat differences between zones. Our results highlight the importance of environmental factors in the composition and abundance of benthic diatoms in tropical aquatic systems.