Is it possible to estimate mass balance in a Storm water drain during bioremediation?

Dear Fellows, I'm working on In-situ Bioremediation in a storm water drain which is receiving domestic sewage from nearby areas where proper sanitation facilities are not available. This drain is not a channelized structure means width and depth are not same along the complete length of 14 Km. It's receiving sewage through 5 lateral lines also. Total flow in the drain is 120 MLD (Million Litre per day). I'm using Bioremediation process with strict and facultative anaerobic bacteria to treat the pollution and bring down BOD and COD up to 20 mg/L and 50 mg/L as per standards of Indian authorities. My question is: Can we calculate Mass balance in such drain where dimensions can't be calculated properly? Secondly the concentrations of major pollutants are also changing tremendously with the flow? If anyone having experience working such project please advice me for the same.