Greenhouse gas emissions from headwater streams are linked to multiple sources influenced by terrestrial land use and hydrology, yet partitioning these sources at catchment scales remains highly unexplored. To address this gap, we sampled year-long stable water isotopes (δ18O and δ2H) from 17 headwater streams differing in catchment agricultural areas. We calculated mean residence times (MRT) and young water fractions (YWF) based on the seasonality of δ18O signals and linked these hydrological measures to catchment characteristics, mean annual water physico-chemical variables, and GHG % saturations. The MRT and the YWF ranged from 0.25 to 4.77 years and 3 to 53%, respectively. The MRT of stream water was significantly negatively correlated with stream slope (r2 = 0.58) but showed no relationship with the catchment area. Streams in agriculture-dominated catchments were annual hotspots of GHG oversaturation, which we attributed to precipitation-driven terrestrial inputs of dissolved GHGs for streams with shorter MRTs and nutrients and GHG inflows from groundwater for streams with longer MRTs. Based on our findings, future research should also consider water mean residence time estimates as indicators of integrated hydrological processes linking discharge and land use effects on annual GHG dynamics in headwater streams.