Harmful algal blooms (HABs) have recently been observed in rivers, including the Illinois River in the Midwest United States. The Illinois River Basin has a history of eutrophication issues, primarily caused by the excessive loading of nitrogen and phosphorus from urban and agricultural sources. Recent events have seen the emergence of cyanobacterial harmful algal blooms in the area. This data release provides early warning indicator (EWI) metrics derived from a continuous chlorophyll concentration dataset obtained from seven water quality monitoring sites along the Illinois River. These metrics include the first-order autoregressive process (Ar1) and the standard deviation (SD) of chlorophyll, which serve as leading indicators of a potential shift in the ecological system, as documented in the ecological literature. For more in-depth information on the methodology used to calculate these metrics and a detailed interpretation of the results as they relate to the Illinois River, please refer to <a href="https://doi.org/10.1016/j.ecolind.2024.111970">Stackpoole et al. 2024</a>. This work was completed as part of the USGS Proxies Project, an effort supported by the Water Mission Area (WMA) Water Quality Processes program to develop estimation methods for PFAS, harmful algal blooms, and metals, at multiple spatial and temporal scales.