Numerous threats to biodiversity exist worldwide, yet long-term trends in species occurrence and distribution are unknown for many species and regions. Recent meta-analyses for some regions highlight diverse species responses to these threats, emphasising the need for species- and region-specific studies. The status of Japan’s biodiversity is globally significant due to its high rate of endemism, yet trends in many species are poorly known. The present study makes novel use of a 20-year ecological dataset collected in and around Japan’s reservoirs, to identify trends in the occurrence and distribution of 360 species, including threatened, invasive, and freshwater-dependent species. Consistent with studies from other regions, the trends were variable and species-specific. Nine percent of species exhibited latitudinal range shifts but the directionality was not consistently polewards, which is often considered the direction that species shift in response to climate change. This highlights the complex interaction among drivers of distributions, and disentangling these should be a consideration for future studies. In addition to confirming known trends in some species, this study identified potential new trends in others. Identifying trends is a first step in addressing biodiversity loss, providing vital information to assess conservation and policy objectives, and the status of biodiversity targets.