A method and system for calculating trading ratios between a buyer and a seller of water quality pollutant load credits. The water quality trading system ("WQTS") inputs a definition of watershed and land uses of the watershed. The WQTS then calculates the load credits (e.g., the difference between total maximum daily load of the pollutant and the actual load needed) of applying various controls (e.g., best management practices and treatments) to the point sources and non-point sources of the watershed. The load credits take into consideration the uncertainty of the calculated loads.