Ecological risk of neonicotinoid insecticides for river ecosystem functions have often been noted; however, empirical support from field observation remains scarce. Here we evaluated the associations of the abundances of the seven functional feeding groups (FFGs) of benthic invertebrate communities with the imidacloprid and dinotefuran concentrations in 2010 in each of four Japanese regions (Eastern Honshu, Central Honshu, Chugoku & Shikoku, and Kyushu). We performed a partial redundancy analysis for each regional dataset of benthic invertebrate communities and environmental variables, which was developed by using the broad-scale biomonitoring and exposure databases. The associations of the abundances of the seven FFGs with the two neonicotinoid concentrations were significant in 2 out of 4 regions, suggesting their non-negligible effects on river ecosystem functions at least in these two regions. Moreover, although the associations in other two regions were insignificant, the negative associations between the imidacloprid concentrations and the abundances of the five FFGs (shredders, filter feeders, collectors, grazers, and predators) seemed to be consistent among four regions, suggesting that these negative associations can also be expected to other regions (i.e., generalizability). Our study suggested the broad-scale effects of imidacloprid use on river ecosystem functions.