Freshwater ecosystems constitute only a small fraction of the planet's water resources, yet support much of its diversity, with freshwater fish accounting for more species than birds, mammals, amphibians or reptiles. Fresh waters are, however, particularly vulnerable to anthropogenic impacts, including habitat loss, climate and land use change, pollution and biological invasions. This environmental degradation, combined with unprecedented rates of biodiversity change, highlights the importance of robust and replicable programmes to monitor freshwater fish. Such monitoring programmes can have diverse aims, including confirming the presence of a single species (e.g., early detection of alien species), tracking changes in the abundance of threatened species, or documenting long‐term temporal changes in entire communities. Irrespective of their motivation, monitoring programmes are only fit for purpose if they have clearly articulated aims and collect data that can meet those aims. This review, therefore, highlights the importance of identifying the key aims in monitoring programmes and outlines the different methods of sampling freshwater fish that can be used to meet these aims. We emphasize that investigators must address issues around sampling design, statistical power, species’ detectability, taxonomy and ethics in their monitoring programmes. Additionally, programmes must ensure that high‐quality monitoring data are properly curated and deposited in repositories that will endure. Through fostering improved practice in freshwater fish monitoring, this review aims to help programmes improve understanding of the processes that shape the Earth's freshwater ecosystems and help protect these systems in face of rapid environmental change.

Ecosystem-based management is costly. Therefore, without rigorously showing that it can outperform traditional species-focused alternatives, its broad-scale adoption in conservation is unlikely. We present a large-scale replicated and controlled set of whole-lake experiments in fish conservation (20 lakes monitored over 6 years with more than 150,000 fish sampled) to examine the outcomes of ecosystem-based habitat enhancement (coarse woody habitat addition and shallow littoral zone creation) versus a widespread, species-focused alternative that has long dominated fisheries management practice (i.e., fish stocking). Adding coarse woody habitats alone did not, on average, enhance fish abundance, but creating shallow water habitat consistently did, especially for juvenile fish. Species-focused fish stocking completely failed. We provide strong evidence questioning the performance of species-focused conservation actions in aquatic ecosystems and instead recommend ecosystem-based management of key habitats.

Swimming performance is a key feature that mediates fitness and survival in aquatic animals. Dispersal, habitat selection, predator–prey interactions and reproduction are processes that depend on swimming capabilities. Testing the critical swimming speed (U_crit) of fish is the most straightforward method to assess their prolonged swimming performance. We analysed the contribution of several predictor variables (total body length, experimental water temperature, time step interval between velocity increments, species identity, taxonomic affiliation, native status, body shape and form factor) in explaining the variation ofU_crit, using linear models and random forests. We compiled in total 204 studies testingU_critof 35 inland fishes of the Iberian Peninsula, including 17 alien species that are non-native to that region. We found that body length is largely the most important predictor ofU_critout of the eight tested variables, followed by family, time step interval and species identity. By contrast, form factor, temperature, body shape and native status were less important. Results showed a generally positive relationship betweenU_critand total body length, but regression slopes varied markedly among families and species. By contrast, linear models did not show significant differences between native and alien species. In conclusion, the present study provides a first comprehensive database ofU_critin Iberian freshwater fish, which can be thus of considerable interest for habitat management and restoration plans. The resulting data represents a sound foundation to assess fish responses to hydrological alteration (e.g. water flow tolerance and dispersal capacities), or to categorize their habitat preferences.

Habitat suitability, dispersal potential, and fragmentation influence the distribution of stream fishes; however, their relative influence and interacting effects on species distributions are poorly understood, which may result in uncertain outcomes of river rehabilitation and conservation. Using empirical data describing 17 relatively common stream fishes, we combine (1) species habitat suitability models (MaxEnt) with a (2) species dispersal model (FIDIMO) and a (3) worst‐case scenario of the influence of river fragmentation on dispersal. Using generalized linear mixed models, we aimed to uncover the role of these factors in explaining the probability of presence. Simulations over nine years allowed for assessing the relative importance of dispersal over time for structuring species occurrences vs. the importance of habitat suitability.Models combining all three structuring factors performed consistently better in predicting the spatial occurrence patterns than models including only single factors. Our results confirmed that distribution patterns of stream fishes are jointly controlled by species dispersal and habitat suitability. An increase of 0.1 habitat suitability probability more than doubled the odds of species occurrence; an increase of 0.1 dispersal probability yielded a 14‐fold increase of the odds of species occurrence. Temporal simulations revealed that over short time frames (1–2 years) dispersal from nearby source populations is four times more important than habitat suitability for species presence. However, over longer time periods, the importance of habitat suitability increases relative to the importance of dispersal. Surprisingly, fragmentation by migration barriers did not appear as a significant driver of occurrence patterns.Concluding, these findings demonstrate the importance of the spatial arrangement of suitable habitats and potential source populations, as well as their relative position in relation to barriers. We emphasize considering the direction of connections within river networks and the dispersal abilities of fishes, as well as providing (access to) new, suitable habitat for successful river rehabilitation.