This data release contains discrete chlorophyll data, specifically corrected chlorophyll a, uncorrected chlorophyll a, and pheophytin pigments, from inland waters in the Illinois River Basin for 1981–2023. These data are discrete samples (collected in the field and analyzed in the laboratory) of plankton (suspended algae) and periphyton (benthic algae) from lakes, streams, rivers, canals, and other aquatic sites. These data support the investigation of harmful algal blooms (HABs) in the Illinois River Basin. The data are multi-source, meaning multiple monitoring organizations collected and analyzed these samples. Data were sourced from the Water Quality Portal (WQP; which contains water quality data from many organizations), Illinois Natural History Survey (INHS), the Fox River Study Group (FRSG; which also contains data from multiple organizations), and previously unpublished data from the US Geological Survey’s National Water Quality Laboratory. Final chlorophyll data are provided in the "all_combined_chl_data.csv" file. Data provided by the INHS included non-chlorophyll water quality data that are published in the "all_other_inhs_data.csv" file. Site information is provided in the "site_list_final.csv" file. The "site_list_original.csv" file provides information for collocated sites that had multiple identifiers (i.e., different site numbers provided by different organizations though samples were all collected at the same physical location). These collocated sites were assigned a single identifier which is used in "site_list_final.csv." Additional details are found in the process steps.