The influence of biogeochemical processes on nitrogen and organic matter transformation and transport was investigated for two urban streams receiving groundwater discharge during the dry summer baseflow period. A multiple lines of evidence approach involving catchment-, and stream reach-scale investigations were undertaken to describe the factors that influence pore water biogeochemical processes. At the catchment-scale gaining stream reaches were identified from water table mapping and groundwater discharge estimated to be between 0.1 and 0.8 m3 m−2 d−1 from baseflow analysis. Sediment temperature profiles also suggested that the high groundwater discharge limited stream water infiltration into the sediments. At the stream reach-scale, dissolved organic carbon (DOC) and dissolved organic nitrogen (DON) concentrations were higher in stream water than in groundwater. However, DOC and DON concentrations were greatest in sediment pore water. This suggests that biodegradation of sediment organic matter contributes dissolved organic matter (DOM) to the streams along with that delivered with groundwater flow. Pore water ammonium (NH4 +) was closely associated with areas of high pore water DOM concentrations and evidence of sulfate (SO4 2−) reduction (low concentration and SO4:Cl ratio). This indicates that anoxic DOM mineralization was occurring associated with SO4 2− reduction. However the distribution of anoxic mineralization was limited to the center of the streambed, and was not constrained by the distribution of sediment organic matter which was higher along the banks. Lower sediment temperatures measured along the banks compared to the center suggests, at least qualitatively, that groundwater discharge is higher along the banks. Based on this evidence anoxic mineralization is influenced by groundwater residence time, and is only measurable along the center of the stream where groundwater flux rates are lower. This study therefore shows that the distribution of biogeochemical processes in stream sediments, such as anoxic mineralization, is strongly influenced by both the biogeochemical conditions and pore water residence time.