Fluorescence and absorbance spectra were measured in discrete surface water samples collected during three sampling campaigns (Nov 2022, Mar/Apr 2023, Jul 2023) on the Illinois Waterway (IWW) and Chicago Area Waterway System (CAWS), which are the primary drainage of the Illinois River Basin (IRB). Water sampling was conducted concurrently with a boat-based water quality mapping effort using the Fast Limnology Automated Measurement (FLAMe) system (Crawford et al., 2015). Each campaign began in the Chicago metropolitan area, and after having sampled Lake Michigan, entered into the upper extent of the IWW, sampling through the CAWS into the lower reaches of the Des Plaines River and finally the Illinois River. After 8-10 days of traveling downriver through the IWW, sampling ended in the Mississippi River upstream of St Louis, Missouri. Discrete water quality samples were collected from various sites that include main channel, tributaries, and off-channel areas (e.g., backwaters) from a depth of 1 meter (m), typically in the center of the channel or aquatic feature. Between 25 and 40 sites were sampled per campaign dependent upon river conditions and boat accessibility. Data reported here are compiled into three tables: 1) full fluorescence spectra in vectorized format, 2) full absorbance spectra, and 3) summary optical measurements commonly used in statistical analyses.