The Bednja River is the longest river flowing with its full course exclusively through Croatia and one of the largest right tributaries of the Drava River, which belongs to the Danube River basin. Due to the variety of habitats present within the course of the Bednja River, as well as older literature reports, it can be expected that this river harbors a high number of freshwater fish species and would likely benefit from conservation and preservation efforts. We compiled and analyzed the existing literature data on the Bednja River fish communities and performed field investigations at various localities on this river in order to describe the current structure of its freshwater fish fauna and monitor changes induced by human activities. Our results corroborate the presence of a rich and diverse fish community. Moreover, with 36 native species, the Bednja River harbors one of the richest fish communities in Croatia as well as in the Danube basin. Unfortunately, modifications of the native fish community were evident in the form of local extinctions, reductions in the population abundance of several native species and the presence of non-native species. Habitat degradation and fragmentation were identified as the most serious threats provoking negative effects on the native fish populations, followed by predatory and competitive effects of invasive species.