Although many studies have focused on marine resources, few studies have considered the resources of inland fisheries. Inland fishery resources are typically either monitored on the basis of catch data alone or are not assessed quantitatively at all, despite their social, economic, and ecological importance. Because freshwater ecosystems have been severely degraded by human activities, evaluating the trends and current status of fishery resources and assessing their drivers are urgent tasks. We compiled long-term data on the annual catch, fishing effort, and fishing power of 23 Japanese lakes, using two sets of government statistics that date back to the 1950s, which were previously neglected because of the large number of missing values. Using Bayesian state-space models, we examined the trajectories of the catch per unit effort (CPUE) of entire communities, considering changes in fishing effort and fishing power, and quantified both changes in the CPUE over the 10-, 20-, and 30-year periods preceding 2008 and the temporal detrended stability of the CPUE over the three periods. We also investigated the relationships among the CPUE changes and stability, anthropogenic drivers, and lake morphometric characteristics. The CPUE declined in 17, 19, and 15 of the 23 lakes over the past 10-, 20-, and 30-year periods, respectively. Our macroecological analyses demonstrate that the functional group richness of exotic piscivores was the most important predictor of changes in the CPUE among the drivers we considered. The stability of the CPUE was positively related to lake area; larger lakes have more stable CPUE. The functional group richness of exotic piscivores also negatively affected the stability of the CPUE. The effect of overfishing was considered to be small because both fishing effort and power declined in almost all of the lakes. Thus, our findings suggest that increasing exotic piscivore species may diminish the resources and their stability, particularly in Japanese lakes where native piscivores are rare. This might lead to a substantial decline in ecosystem services. Our study highlights the importance of assessing inland fishery resources in a comprehensive manner and the need for restoration strategies to mitigate the effects of exotic piscivores.