Temporal and Spatial Dynamics of the Lotic Fish Communities: A Comparison of Coffee Filter‐Based Passive e<scp>DNA</scp> Collection Versus Active e<scp>DNA</scp> Filtering

ABSTRACT Environmental DNA (eDNA) metabarcoding is a noninvasive and cost‐effective method for fish community monitoring, enabling the determination of both the presence/absence of fish species and their relative quantity in closed systems. However, the integration of these novel eDNA‐based methods into current monitoring practices is not straightforward and require standardization of methodological approaches. In this study, we investigated spatial and temporal variation in fish assemblages within two lotic systems in Croatia. Six sampling stations were located alongside the middle section of the river Sava upstream and downstream of Zagreb, and one location in the stream Okićnica. We compared traditional field surveys with two eDNA sampling methodologies: active eDNA filtering and passive eDNA collection. We showed that passive eDNA collection using coffee filters detected fish composition as effectively as active eDNA filtration, providing comparable results in terms of local species richness and spatial variation in fish assemblages. Generally, our eDNA approach detected a greater fish species richness per site than electrofishing. Each single sample captured an average of 18.3 species, from a total of 30 species encountered in the 78 samples. The sites upstream of Zagreb showed significant differences in species read abundance in comparison to the sites downstream. Nonmetric multidimensional scaling (nMDS) plot based on read abundance appeared to be structured according to the type of lotic system, with a clear separation in the two‐dimensional space between samples from the river Sava and stream Okićnica and between seasons. A substantial increase in read abundance during spawning periods of certain species was observed, emphasizing the method's utility in unraveling ecological complexities. Altogether, this study exemplifies how eDNA metabarcoding is a powerful tool for community monitoring, providing standardized information that will be valuable for environmental management.