The main objective of this study was to analyze the spatial and temporal variability of dissolved organic matter (DOM) in an urban setting, identify its drivers and analyze the potential of DOM as a monitoring tool. We sampled at 32 sites within the city of Berlin (Germany) during 4 different seasons in 2016 and 2017. Sites included rivers, streams, ponds, and lakes. We here present the data used for the study, including the DOM composition parameters and the physico-chemical variables. DOM composition included the Absorbance/Fluorescence analysis, PARAFAC modelling and the indexes from the ultrahigh-resolution Fourier-Transform Ion Cyclotron Mass Spectrometry (FT-ICR-MS) measurements. The physicochemical variables included nutrients and land use.