Abstract. Anthropogenic activities increase the contributions of inland waters to global greenhouse gas (GHG; CO2, CH4, and N2O) budgets, yet the mechanisms driving these increases are still not well constrained. In this study, we quantified year-long GHG concentrations and fluxes, as well as water physico-chemical variables from 23 streams, 3 ditches, and 2 wastewater inflow sites across five headwater catchments in Germany contrasted by land use. Using mixed-effects models, we determined the overall impact of land use and seasonality on the intra-annual variabilities of these parameters. We found that land use was more significant than seasonality in controlling the intra-annual variability of GHG concentrations and fluxes. Agricultural land use and wastewater inflows in settlement areas resulted in up to 10 times higher daily riverine CO2, CH4, and N2O emissions than forested areas, as substrate inputs by these sources appeared to favor in situ GHG production processes. Dissolved GHG inputs directly from agricultural runoff and waste-water inputs also contributed substantially to the annual emissions from these sites. Drainage ditches were hotspots for CO2 and CH4 fluxes due to high dissolved organic matter concentrations, which appeared to favor in situ production via respiration and methanogensis. Overall, the annual emission from anthropogenic-influenced streams in CO2-equivalents was up to 20 times higher (~71 kg CO2 m-2 yr-1) than from natural streams (~3 kg CO2 m-2 yr-1). Future studies aiming to estimate the contribution of lotic ecosystems to GHG emissions should therefore focus on anthropogenically perturbed streams, as their GHG emission are much more variable in space and time.