The European Water Framework Directive 2000/60/EC (WFD) has been implemented over the past 20 years, using physicochemical, biological and hydromorphological elements to assess the ecological status of surface waters. Benthic diatoms (i.e., phytobenthos) are one of the most common biological quality elements (BQEs) used in surface water monitoring and are particularly successful in detecting eutrophication, organic pollution and acidification. Herein, we reviewed their implementation in river biomonitoring for the purposes of the WFD, highlighting their advantages and disadvantages over other BQEs, and we discuss recent advances that could be applied in future biomonitoring. Until now, phytobenthos have been intercalibrated by the vast majority (26 out of 28) of EU Member States (MS) in 54% of the total water bodies assessed and was the most commonly used BQE after benthic invertebrates (85% of water bodies), followed by fish (53%), macrophytes (27%) and phytoplankton (4%). To meet the WFD demands, numerous taxonomy-based quality indices have been developed among MS, presenting, however, uncertainties possibly related to species biogeography. Recent development of different types of quality indices (trait-based, DNA sequencing and predictive modeling) could provide more accurate results in biomonitoring, but should be validated and intercalibrated among MS before their wide application in water quality assessments.

The hydrological and biological complexity of temporary rivers as well as their importance in providing goods and services is increasingly recognized, as much as it is the vulnerability of the biotic communities in view of climate change and increased anthropogenic pressures. However, the effects of flow intermittency (resulting from both seasonal variations and rising hydrological pressure) and pollution on biodiversity and ecosystem functioning have been overlooked in these ecosystems. We explore the way multiple stressors affect biodiversity and ecosystem functioning, as well as the biodiversity-ecosystem functioning (B-EF) relationship in a Mediterranean temporary river. We measured diversity of benthic communities (i.e. diatoms and macroinvertebrates) and related ecosystem processes (i.e. resource use efficiency-RUE and organic matter breakdown-OMB) across a pollution and flow intermittency gradient. Our results showed decreases in macroinvertebrate diversity and the opposite trend in diatom assemblages, whereas ecosystem functioning was negatively affected by both pollution and flow intermittency. The explored B-EF relationships showed contrasting results: RUE decreased with higher diatom diversity, whereas OMB increased with increased macroinvertebrate diversity. The different responses suggest contrasting operating mechanisms, selection effects possibly driving the B-EF relationship in diatoms and complementarity effects driving the B-EF relationship in macroinvertebrates. The understanding of multiple stressor effects on diversity and ecosystem functioning, as well as the B-EF relationship in temporary rivers could provide insights on the risks affecting ecosystem functioning under global change.

The biodiversity–ecosystem functioning (BEF) relationship has been studied extensively for the past 30 years, mainly in terrestrial plant ecosystems using experimental approaches. Field studies in aquatic systems are scarce, and considering primary producers, they mainly focus on phytoplankton assemblages, whereas benthic diatoms in rivers are considerably understudied in this regard. We performed a field study across nine rivers in Greece, and we coupled the observed field results with model simulations. We tested the hypothesis that the diversity–biomass (as a surrogate of ecosystem functioning) relationship in benthic diatoms would be affected by abiotic factors and would be time-dependent due to the highly dynamic nature of rivers. Indeed, geology played an important role in the form of the BEF relationship that was positive in siliceous and absent in calcareous substrates. Geology was responsible for nutrient concentrations, which, in turn, were responsible for the dominance of specific functional traits. Furthermore, model simulations showed the time dependence of the BEF form, as less mature assemblages tend to present a positive BEF. This was the first large-scale field study on the BEF relationship of benthic diatom assemblages, offering useful insights into the function and diversity of these overlooked ecosystems and assemblages.

The Prespa Lakes system, shared between Greece, the Republic of North Macedonia, and Albania, forms a significant transboundary, large-scale integrated freshwater ecosystem subject to multiple anthropogenic and natural pressures. This study focuses on the Greek part of the Prespa Lakes system with particular emphasis on the identification of the ecological and hydrological impacts of the contributing stream inflows on the lakes by examining the spatial variability in physicochemical and biological conditions and conducting water balance and isotopic analyses. Based on our results, streams draining into Lesser Prespa Lake exhibited more pronounced hydrological and physicochemical fluctuations than the Agios Germanos River connected to Great Prespa Lake, while ecological status classifications of all studied streams ranged from high to moderate. Furthermore, moderate ecological status conditions (mainly observed at the downstream stations) were closely associated with adjacent anthropogenic pressures, including agricultural drainage, livestock activities, irrigated croplands, and wastewater discharges. In addition, although both lakes were classified as mesotrophic, field data indicated greater transparency loss in Lesser Prespa than in Great Prespa Lake. Regarding the stream influences on Lesser Prespa Lake’s water quality, nutrient loads induced changes in lake concentrations by roughly one month. Total nitrogen showed moderate stream–lake correlations (R = 0.61) and a strong negative correlation for total phosphorus (R = −0.94), suggesting substantial nutrient retention and processes within the lake. Water balance analysis revealed an annual water deficit for both Lesser and Great Prespa, with the latter exhibiting a markedly stronger and systematic long-term decline in water level. In the Lesser Prespa, seasonal fluctuations in water volume were primarily driven by excess rainfall, while stream inflows contributed minimally. Conversely, correlation analysis for Great Prespa identified surface inflow from the Ag. Germanos catchment as the dominant driver of water storage variability, surpassing direct rainfall, with strong correlations in both wet (R = 0.79) and dry (R = 0.88) periods. Isotopic compositions (δ¹⁸O, δ²H) did not differ significantly between the two lakes, indicating common recharge sources and strong evaporative imprints, while stream isotopic signatures highlighted spatial and seasonal variability in hydrological inputs. Seasonal and spatial variations were proved to be strongly influenced by both natural hydrological dynamics and anthropogenic pressures within the basin, while these findings reinforce the importance and the necessity of adopting holistic, cross-border management strategies that maintain the ecological integrity and the long-term sustainability of the Prespa Lakes ecosystem.

Coastal ecosystems typically comprise water patches of different salinities that host distinct communities of species. This salinity-driven heterogeneity can be vulnerable to changes in between-patch connectivity due to altered water levels. Despite the potentially grave implications for higher trophic levels, the impact of increased connectivity on phytoplankton assemblages is largely unknown. Here, we investigate the effect of increasing connectivity on assemblage resistance and recovery along a strong salinity gradient of 40-61 psu. We deployed mesocosms within a saltwork system and hydraulically connected enclosures of 3 salinity levels at 3 connectivity levels. We hypothesized that assemblage composition of high salinity would be more resistant to press invasions during connectivity; however, high connectivity would decrease compositional resistance and recovery irrespective of salinity. We found that high salinity assemblages were indeed more resistant and recovered better at low connectivity. High connectivity also impacted the function of high salinity assemblages by replacing large diatoms with small flagellates, preventing assemblage recovery. Counterintuitively, low salinity assemblage composition recovered better at higher connectivity, and this was attributed to rescue effects of rarer and stenohaline species within a more variable nutrient environment. Here, we show that normal (i.e. marine) salinity assemblages are vulnerable to anticipated changes in coastal hydrological regimes whereas higher salinity assemblages are impacted above a certain connectivity threshold.