Many field-survey projects have been conducted for many decades to obtain empirical information about the negative effects of nickel (Ni) pollution on the biological integrity of river ecosystems. However, as field surveys need a large amount of effort, field survey sites of each project tend to be limited to a small number of basins. Thus, the average size of the effect of intervention in Ni concentrations on aquatic organisms across Japanese rivers have rarely been evaluated. In the present study, to evaluate the average effect size of Ni pollution on aquatic organisms in Japanese rivers, we constructed a dataset of benthic invertebrate communities and environmental variables by using the following two nationwide-scale databases: the River Environmental Database and the database of water quality measurements for public water bodies (provided by the Ministry of Land, Infrastructure, Transport and Tourism and the Ministry of Environment, respectively). Using the developed dataset, we examined the associations of structural measures of benthic invertebrate communities with Ni concentrations.