Conventional effluent trading systems (ETSs) between point sources (PSs) and nonpoint sources (NPSs) are often unreliable because of the uncertain characteristics of NPSs. In this study, a new framework was established for PS-NPS ETSs, and a comprehensive analysis was conducted by quantifying the impacts of the uncertainties associated with the water assimilative capacity (WAC), NPS emissions, and measurement effectiveness. On the basis of these results, the uncertain characteristics of NPSs would result in a less cost-effective PS-NPS ETS during most hydrological periods, and there exists a clear transition occurs from the WAC constraint to the water quality constraint if these stochastic factors are considered. Specifically, the emission uncertainty had a greater impact on PSs, but an increase in the emission or abatement uncertainty caused the abatement efforts to shift from NPSs toward PSs. Moreover, the error transitivity from the WAC to conventional ETS approaches is more obvious than that to the WEFZ-based ETS. When NPSs emissions are relatively high, structural BMPs should be considered for trading, and vice versa. These results are critical to understand the impacts of uncertainty on the functionality of PS-NPS ETSs and to provide a trade-off between the confidence level and abatement efforts.