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Abstract. Water quality models serve as an economically feasible alternative to quantify fluxes of nutrient pollution and to simulate effective mitigation strategies; however, their applicability is often questioned due to broad uncertainties in model structure and parameterization, leading to uncertain outputs. We argue that reduction of uncertainty is partially achieved by integrating stable isotope data streams within the water quality model architecture. This article outlines the use of stable isotopes as a response variable within water quality models to improve the model boundary conditions associated with nutrient source provenance, constrain model parameterization, and elucidate shortcomings in the model structure. To assist researchers in future modeling efforts, we provide an overview of stable isotope theory; review isotopic signatures and applications for relevant carbon, nitrogen, and phosphorus pools; identify biotic and abiotic processes that impact isotope transfer between pools; review existing models that have incorporated stable isotope signatures; and highlight recommendations based on synthesis of existing knowledge. Broadly, we find existing applications that use isotopes have high efficacy for reducing water quality model uncertainty. We make recommendations toward the future use of sediment stable isotope signatures, given their integrative capacity and practical analytical process. We also detail a method to incorporate stable isotopes into multi-objective modeling frameworks. Finally, we encourage watershed modelers to work closely with isotope geochemists to ensure proper integration of stable isotopes into in-stream nutrient fate and transport routines in water quality models. Keywords: Isotopes, Nutrients, Uncertainty analysis, Water quality modeling, Watershed.