In this study we analysed a regulated European Central river (Moselle) over a course of two years with contrasting hydrological conditions. The year 2021 was characterized by cooler water temperatures, higher discharge and flow velocity in comparison to the warmer, low flow year 2022. To study the impacts on water quality and cyanobacterial dynamics, we were using a multidisciplinary approach: weekly in situ biochemical data, longitudinal profiles, hydrological modelling and remote sensing of chlorophyll. This dataset consists of weekly physico-chemical, nutrient and chlorophyll-a measurements in Koblenz (Germany) as well as two longitudinal profiles over a gradient of 240 river kilometre in late summer in 2021 and 2022, respectively.