This study evaluated nutrient flux (nitrate (NO3−), ammonium (NH4+), phosphate (PO43−), and dissolved organic carbon (DOC) at the sediment-water interface and river ecosystem metabolism (REM) to investigate how these ecological functions vary in Beijing’s urban waterways. Three tributaries of the River Beiyun were selected. Water quality varied across the study sites as each receives a mixture of wastewater treatment plant (WWTP) effluents and tributary inflows. A chamber technique was applied where water-specific nutrient concentrations were measured at two exposure times (3 and 10 min). Under the actions of physical and biological processes, NO3− and NH4+ flux was primarily controlled by equilibrium concentration and the N-cycle. However, bioabsorption appeared to regulate DOC flux. Specifically, NO3− flux ranged from −0.31 to +0.30 mg/(m2·s), NH4+ was −0.01 to +0.05 mg/(m2·s), PO43− was −0.01 to +0.01 mg/(m2·s), DOC was −0.04 to +0.13 mg/(m2·s). We applied the nighttime slope regression to estimate gross primary production (GPP) and ecosystem respiration (ER). Except in summer, net ecosystem production (GPP+ER) less than 0 indicated heterotrophic study reaches. Structural equation modelling revealed that nutrient dynamics and water temperature were the primary factors driving REM. Our study provides the needed systems-based understanding of vital ecological processes to improve in-stream management.