Water quality trading between point and diffuse sources aims to improve waterway health and achieve sustainable management goals for aquatic ecosystems. However, methods are needed to quantitatively compare their ecosystem impacts. Our study used a key measure of ecosystem health, dissolved oxygen (DO) demand, to identify and compare the nutrient and organic carbon parameters in different nutrient sources that have the greatest impact on DO demand. Three nutrient sources, i.e., simulated soil erosion runoff (soil slurries), sewage treatment plant (STP) and aquaculture effluent, were compared in incubations measuring DO demand in estuarine water. For soil slurries, dissolved organic carbon (DOC) concentration was most highly correlated with DO demand (R2 = 0.52). For STPs, a combination of total nitrogen (TN), phosphate, and ratios of TN: total phosphorus and DOC: ammonium were most correlated with DO demand (R2 = 0.5). The combination of chlorophyll-a concentrations and DOC: total dissolved nitrogen explained most of the DO demand for aquaculture treatments (R2 = 0.80). Chemical characterization revealed that soil slurries contained organic compounds that were more bioavailable, i.e., glucose and fatty acids, than STP (small organic acids) and aquaculture effluents (lipophilic compounds). DOC bioreactivity (mg DO mg−1 DOC d−1) of the three sources correlated with C:N ratios and N:P ratios, suggesting that microbes in the estuarine water were organic carbon and nutrient limited. Therefore, to ensure equitable environmental impacts from trading between different sources, both organic carbon and nutrient parameters from sources, and the nutrient characteristics of the receiving water environment need to be considered.