Precipitation occurs in two basic forms defined as liquid state and solid state. Different from rain-fed watershed, modeling snow processes is of vital importance in snow-dominated watersheds. The seasonal snowpack is a natural water reservoir, which stores snow water in winter and releases it in spring and summer. The warmer climate in recent decades has led to earlier snowmelt, a decline in snowpack, and change in the seasonality of river flows. The Soil and Water Assessment Tool (SWAT) could be applied in the snow-influenced watershed because of its ability to simultaneously predict the streamflow generated from rainfall and from the melting of snow. The choice of parameters, reference data, and calibration strategy could significantly affect the SWAT model calibration outcome and further affect the prediction accuracy. In this study, SWAT models are implemented in four upland watersheds in the Tulare Lake Basin (TLB) located across the Southern Sierra Nevada Mountains. Three calibration scenarios considering different calibration parameters and reference datasets are applied to investigate the impact of the Parallel Energy Balance Model (ParBal) snow reconstruction data and snow parameters on the streamflow and snow water-equivalent (SWE) prediction accuracy. In addition, the watershed parameters and lapse rate parameters-led equifinality is also evaluated. The results indicate that calibration of the SWAT model with respect to both streamflow and SWE reference data could improve the model SWE prediction reliability in general. Comparatively, the streamflow predictions are not significantly affected by differently lumped calibration schemes. The default snow parameter values capture the extreme high flows better than the other two calibration scenarios, whereas there is no remarkable difference among the three calibration schemes for capturing the extreme low flows. The watershed and lapse rate parameters-induced equifinality affects the flow prediction more (Nash-Sutcliffe Efficiency (NSE) varies between 0.2–0.3) than the SWE prediction (NSE varies less than 0.1). This study points out the remote-sensing-based SWE reconstruction product as a promising alternative choice for model calibration in ungauged snow-influenced watersheds. The streamflow-reconstructed SWE bi-objective calibrated model could improve the prediction reliability of surface water supply change for the downstream agricultural region under the changing climate.