Here we presented two datasets (biological and environmental datasets) collected in a comprehensive large geographical scale (approximately 1.1×105 km2) survey of rivers/streams in the Haihe River Basin (HRB), which has become the most polluted river basin in past two decades in China. The survey selected a total of 94 representative sampling sites in the plain region of HRB, where environmental pollution is more severe than the mountain region. The biological dataset contains the information on the identified rotifer species and their abundance, while the environmental dataset provides the measured environmental variables at each sampling site. Based on this ecological survey, we identified a total of 91 rotifer species and their abundance, as well as abundance of two crucial taxonomic groups on rotifers' food webs (i.e., protozoans and crustaceans), and also presented seven environmental variables, particularly those associated with nitrogen and phosphorus pollution.