The inheritance of historic human-induced disruption and the fierceness of its impact change aquatic ecosystems. This work reviews some of the main stressors on freshwater ecosystems, focusing on their effects, threats, risks, protection, conservation, and management elements. An overview is provided on the water protection linked to freshwater stressors: solar ultraviolet radiation, thermal pollution, nanoparticles, radioactive pollution, salinization, nutrients, sedimentation, drought, extreme floods, fragmentation, pesticides, war and terrorism, algal blooms, invasive aquatic plants, riparian vegetation, and invasive aquatic fish. Altogether, these stressors build an exceptionally composite background of stressors that are continuously changing freshwater ecosystems and diminishing or even destroying their capability to create and maintain ongoing natural healthy products and essential services to humans. Environmental and human civilization sustainability cannot exist without the proper management of freshwater ecosystems all over the planet; this specific management is impossible if the widespread studied stressors are not deeply understood structurally and functionally. Without considering each of these stressors and their synergisms, the Earth’s freshwater is doomed in terms of both quantitative and qualitative aspects.

Rivers are experiencing increasing anthropogenic pressures and salinity has shown to affect freshwater fish behaviour, potentially disrupting ecological processes. In this study, the aim was to determine the sub-lethal effects of salinization on freshwater fish behaviour, using a widespread native cyprinid species, the Iberian barbel (Luciobarbus bocagei) as the model species. Behavioural trials in a mesocosms setting were performed to assess the effects of three levels of a salinity gradient - control (no salt added to the water, 0.8 mS/cm), low (9 mS/cm), and high concentration (18 mS/cm) - on fish routine activity, shoal cohesion and boldness. Upon increasing the salinity levels in the flume-channels, fish showed a significant reduction on their i) swimming activity (76% of searching behaviour in the control vs. 57% in high salinity), and ii) shoal cohesion (0.95 shoal cohesion ratio in the control vs. 0.76 in high salinity), while iii) an increase of bolder individuals, measured by a higher number of attempts to escape the altered environment (106 total jumps in the control vs. 262 in high salinity), was simultaneously observed. Behavioural changes in fish can reflect shifts in ecological condition. Thus, the behavioural responses of fish caused by salinization stress should be further researched, in addition to the interaction with other environmental stressors, in order to understand the true scope of the consequences of salinization for fish species.

River ecosystems are exposed to a multitude of stressors, including increasing pesticide run-off driven by precipitation and irrigation. Pyrethroids are the fourth major group of insecticides in use worldwide and have extremely negative effects on aquatic fauna. In this study, we aimed to assess the effects of an acute 2 h sub-lethal exposure to different levels of the pyrethroid esfenvalerate on the swimming behaviour of two Cypriniformes species: the native Iberian barbel (Luciobarbus bocagei) and the non-native invasive bleak (Alburnus alburnus). The experimental set-up consisted of previous exposure to three esfenvalerate concentrations (control, 1.2 (low), and 2.0 (high) μg/L) before being stocked in a three-artificial-flume-channel mesocosm for behavioural trials through direct observation. Monitored behaviours included (i) routine activity, (ii) shoal cohesion, and iii) boldness. Significant differences in fish behaviour were detected for the native species (barbel), as individuals spent significantly more time holding position (i.e., resting) in the control (44.9%) than in the high esfenvalerate concentration (25.2%). Concordantly, control barbels were also found to perform more directional changes than the ones exposed to high esfenvalerate concentrations. Behavioural changes were also found for boldness, measured by the proportion of fish attempts to negotiate the upstream ramp, which were significantly higher in the control (37.4%) and in the high concentration (41.5%) compared to the low one (21.1%). Finally, regarding shoal cohesion of the barbel, it was tighter in the control (81.3%) than in the low- (70.5%) and high- (71.1%) esfenvalerate treatments. For the invasive bleak, there were no significant differences in any of the behavioural traits upon previous exposure to an increasing esfenvalerate concentration. This experimental study demonstrated that even short-term exposure to the pyrethroid esfenvalerate was sufficient to alter the behaviour of a native Cypriniformes fish species while not affecting the non-native species. This may confer greater competitive advantages to non-native fish species in the context of global changes.

Freshwater habitats and biota are among the most threatened worldwide. In Europe, significant efforts are being taken to counteract detrimental human impacts on nature. In line with these efforts, the MERLIN project funded by the H2020 program focuses on mainstreaming ecosystem restoration for freshwater-related environments at the landscape scale. Additionally, the Dammed Fish project focuses on one of the main threats affecting European Networks—artificial fragmentation of the river. Meeting the objectives of both projects to work on a large, pan-European scale, we developed a novel spatial database for river units. These spatial units, named River Restoration Units (R2Us), abide by river network functioning while creating the possibility of aggregating multiple data sources with varying resolutions to size-wise comparable units. To create the R2U, we set a methodological framework that departs from the Catchment Characterization and Modelling—River and Catchment Database v2.1 (CCM2)—together with the capabilities of the River Network Toolkit (v2) software (RivTool) to implement a seven-step methodological procedure. This enabled the creation of 11,557 R2U units in European sea outlet river basins along with their attributes. Procedure outputs were associated with spatial layers and then reorganized to create a relational database with normalized data. Under the MERLIN project, R2Us have been used as the spatial analysis unit for a large-scale analysis using multiple input datasets (e.g., ecosystem services, climate, and European Directive reporting data). This database will be valuable for river management and conservation planning, being particularly well suited for large-scale restoration planning in accordance with European Nature legislation.

In Europe, ecological restoration efforts remain restricted and fragmented, with limited success and coordination across policies. The newly adopted Nature Restoration Regulation aims to address these challenges by setting ambitious, legally binding restoration targets. For freshwater ecosystems, its success depends on better integration of existing legislative frameworks, particularly the Habitats Directive (HD) and the Water Framework Directive (WFD). We present a novel European-scale modeling framework that for the first time, combines HD and WFD-related indicators, and applies specific Bayesian Network features, to achieve: i) a Europe-wide status prediction to identify areas with potential for restoration, conservation or mitigation measures, including spatially explicit information on uncertainty and data gaps, and ii) spatially explicit restoration targets, such as lateral and longitudinal connectivity improvements, derived through backward inference. Model validation demonstrated acceptable performance for six of twelve HD groups, including Bogs, Mires, Fens, as well as Amphibia, Fish and Plants, while sensitivity analysis indicated that taxon-specific responses were primarily driven by pressures from hydrology, morphology, and organic pollution. We provide a large-scale data-driven tool to maximize the ecological impact of restoration efforts across Europe, support efficient resource use, and help policymakers to direct efforts where they are most likely to succeed.