AbstractBy utilizing functional relationships based on observations at plot or field scales, water quality models first compute surface runoff and then use it as the primary governing variable to estimate sediment and nutrient transport. When these models are applied at watershed scales, this serial model structure, coupling a surface runoff sub‐model with a water quality sub‐model, may be inappropriate because dominant hydrological processes differ among scales. A parallel modeling approach is proposed to evaluate how best to combine dominant hydrological processes for predicting water quality at watershed scales. In the parallel scheme, dominant variables of water quality models are identified based entirely on their statistical significance using time series analysis. Four surface runoff models of different model complexity were assessed using both the serial and parallel approaches to quantify the uncertainty on forcing variables used to predict water quality. The eight alternative model structures were tested against a 25‐year high‐resolution data set of streamflow, suspended sediment discharge, and phosphorous discharge at weekly time steps. Models using the parallel approach consistently performed better than serial‐based models, by having less error in predictions of watershed scale streamflow, sediment and phosphorus, which suggests model structures of water quantity and quality models at watershed scales should be reformulated by incorporating the dominant variables. The implication is that hydrological models should be constructed in a way that avoids stacking one sub‐model with one set of scale assumptions onto the front end of another sub‐model with a different set of scale assumptions.