Diurnal variations in physical and chemical concentrations, including nutrients, are observed in river ecosystems. Understanding these cycles and separating the effects of physical loading (from point and non-point sources) and biogeochemical processes are necessary for water management and the TMDL process. A chloride mass balance approach is used to separate the relative influences of physical loading and biogeochemical processes in the Bow River through Calgary, Canada, which has a significant influence on the river water chemistry. Sampling campaigns were conducted in December 2005, when minimal photosynthesis and respiration occur, and in July 2006, when river discharge is high and some photosynthesis and respiration activity is present. Samples in each campaign were collected at point source input and output along the river reach through the city every hour for a 24-hour period, allowing for time of travel. The two wastewater treatment facilities within the city contributed the majority of physical mass loading to the river, with temporal variations in effluent discharge, chloride, and nutrient concentrations. Wastewater effluent chloride to nutrient (as well as other parameter relationships) concentrations also varied diurnally. An hourly chloride mass balance was achieved, within 0.5% (average, S.D.=4.4) for December and 7.7% (average, S.D.=4.2) for July, between estimated cumulative sum values from all inputs and measured values at the river output downgradient of the city, allowing for the investigation of other parameter conservativeness. Some slight diurnal variations associated with photosynthesis and respiration were observed even with limited productivity in the river. Nitrate mass fluxes appeared to be most strongly influenced by photosynthesis and respiration processes, with phosphate being less influenced. Ammonia mass fluxes appeared to be most strongly influenced by wastewater effluent loading. Physical loading can mask or enhance biogeochemical diurnal fluctuations, creating errors in river process interpretations. Chloride was a useful tracer in the mass balance to distinguish between and assist in separating physical loading and biogeochemical processes in the river.