Here, we studied two Dutch rivers which both receive municipal wastewater effluent; river Linge and river Kromme Rijn. Dissolved concentrations and fluxes of CH4, N2O and CO2 were measured upstream, downstream and at discharge locations, alongside water column properties and sediment composition. Microbial communities in the sediment and water column were analysed using 16S rRNA gene sequencing. Microbial data will be stored on the European Nucleotide Archive.