Discussion
Our study demonstrates that eDNA metabarcoding is a useful tool for the assessment of fish diversity in spatially heterogeneous temperate water bodies. This novel molecular approach can be used to provide baseline data for reliable and sustainable long‐term monitoring of these systems. The studied reservoirs exemplify heterogeneous water bodies with pronounced environmental gradients affecting spatial distribution of organisms that is not easy to capture with conventional monitoring methods. In this study, weather conditions during sample collection were typical for temperate regions, with a hot dry summer followed by cold wet autumn. The morphology of the studied reservoirs is similar, but their trophic status and hydrodynamics are different. However, despite such complex background variation, similar ecological relationships between biological and environmental factors were detected in different water bodies. Our results can therefore be used as an example of the applications for other heterogeneous systems.