We investigate the fidelity of the Delta Simulation Model-2 (DSM2), a one-dimensional branched network hydrodynamics solver, which is used to model water quality and ecology in the Sacramento–San Joaquin Delta estuary. We find that while DSM2 reproduces the total flows well, it does not accurately represent the harmonic components of the tides and tidal modulation of subtidal flow. The inaccurate representation of tidal dynamics affects prediction of subtidal flows, flow splits at key junctions, and salinity. These deviations are the result of coarse spatial and temporal representation of tides as well as unrepresented estuarine physical processes. We propose and evaluate two types of schemes intended to improve fidelity: modifying the model domain and specifying fine grid and boundary conditions, and incorporating and parameterizing more complex physical processes into the 1-D model. We also develop a comprehensive protocol to evaluate the model in which we assess the fidelity of model results. In this protocol, we also include a decomposition of the model error into a systematic component because of model representation, and an unsystematic component, which includes errors from both unmodeled physical processes and data precision. Our analysis reveals that these recommendations would be effective provided they can be incorporated with model recalibration. Both our proposed schemes and the model evaluation process will be useful in analyzing models of networked surface water systems such as the Delta in which the distribution of observations is spatially inhomogeneous.

In branching channel networks, such as in the Sacramento–San Joaquin River Delta, junction flow dynamics contribute to dispersion of ecologically important entities such as fish, pollutants, nutrients, salt, sediment, and phytoplankton. Flow transport through a junction largely arises from velocity phasing in the form of divergent flow between junction channels for a portion of the tidal cycle. Field observations in the Georgiana Slough junction, which is composed of the North and South Mokelumne rivers, Georgiana Slough, and the Mokelumne River, show that flow phasing differences between these rivers arise from operational, riverine, and tidal forcing. A combination of Acoustic Doppler Current Profile (ADCP) boat transecting and moored ADCPs over a spring–neap tidal cycle (May to  June 2012) monitored the variability of spatial and temporal velocity, respectively. Two complementary drifter studies enabled assessment of local transport through the junction to identify small-scale intrajunction dynamics. We supplemented field results with numerical simulations using the SUNTANS model to demonstrate the importance of phasing offsets for junction transport and dispersion. Different phasing of inflows to the junction resulted in scalar patchiness that is characteristic of MacVean and Stacey’s (2011) advective tidal trapping. Furthermore, we observed small-scale junction flow features including a recirculation zone and shear layer, which play an important role in intra-junction mixing over time scales shorter than the tidal cycle (i.e., super-tidal time scales). The study period spanned open- and closed-gate operations at the Delta Cross Channel. Synthesis of field observations and modeling efforts suggest that management operations related to the Delta Cross Channel can strongly affect transport in the Delta by modifying the relative contributions of tidal and riverine flows, thereby changing the junction flow phasing.