Tributary source water provenance is a primary control on water quality and ecological characteristics in branching tidal river systems. Source water provenance can be estimated both from field observations of chemical characteristics of water and from numerical modeling approaches. This paper highlights the strengths and shortcomings of two methods. One method uses stable isotope compositions of oxygen and hydrogen from water in field-collected samples to build a mixing model. The second method uses a calibrated hydrodynamic model with numerical tracers released from upstream reaches to estimate source-water fraction throughout the model domain. Both methods were applied to our study area in the eastern Sacramento–San Joaquin Delta, a freshwater tidal system which is dominated by fluvial processes during the flood season. In this paper, we show that both methods produce similar source water fraction values, implying the usefulness of both despite their shortcomings, and fortifying the use of hydrodynamic tracers to model transport in a natural system.