The dataset contains yearlong monthly measurements (June 2020 to April 2022) of water quality parameters, CO2, CH4 and N2O concentrations from 23 streams, 3 drainage ditches and 2 wastewater effluent sites within within the Loisach, Schwingbach and Neckar catchments in Germany. The study sites covered various upstream land uses (croplands, wetlands, grasslands, settlements and forests) as well as stream orders (1-6). Measurements were mostly done during the day between 8.00 am and 5.00pm.