We monitored suspended chlorophyll concentration and turbidity during 48 storm events at two locations with contrasting hydraulic storage caused by milldams between the sites. Our study provides 15-min interval data on river flow, temperature, turbidity and chlorophyll-a concentration for each one of these events. These data have undergone a QA/QC process in which fouling drift was corrected by applying an offset linear interpolation before and after cleaning, and a discrete analytical correction was also applied based on extracted-chlorophyll analysis from grab samples. The dataset is provided in a wide csv format with one parameter per column.