Watershed‐scale hydrologic models are commonly used to assess the water quality effects of agricultural conservation practices that improve soil health (e.g., cover crops and no‐till). However, models rarely account for how these practices (i.e., soil health practices) affect soil physical and functional properties such as water holding capacity and soil aggregate stability, which may, in turn, affect water quality. We introduce a method to represent changes in soil physical and functional properties caused by soil health practices in the Soil and Water Assessment Tool (SWAT) model. We used the SWAT model's default representation of winter cover crops and no‐till and modified soil descriptive parameters to depict soil health practice effects on soil properties. We assumed that the soil health practices would increase soil organic carbon (SOC), a principal indicator of soil health, by 0.01 g C g–1 of soil and then estimated changes in other soil properties (e.g., water holding capacity) using SOC‐based predictive equations and preceding literature. Results indicated that our soil property modifications had statistically significant effects on simulated hydrology and nutrient loss, though outputs were more substantially affected by the model's default representation of cover crops and no‐till. Results also indicated that soil health practices can reduce nitrogen and total phosphorus loss but may increase dissolved reactive phosphorus loss. Our representation of soil health practices provides a more complete estimate of practice efficacy but underscores a need for additional observational data to verify results and guide further model improvements.