This dataset is part of a study investigating the impact of high and low flow in the central European River Moselle on water quality and cyanobacterial dynamics. It includes 23 samplings point along 240 km of the German part of the River Moselle in the respective summers of 2021 and 2022. At each sampling point water samples were taken for physico-chemical data (Conductivity, pH, Oxygen), nutrients (NH4, oPO4, Si, TN, TP), carbon (TOC, DOC), Microcystis cell numbers and chlorophyll-a measurements.