Where rivers encounter estuaries, a transition zone develops where riverine and tidal processes both affect sediment transport processes. One such transition zone is the Sacramento‐San Joaquin River Delta, a large, complex system where several rivers meet to form an estuary (San Francisco Bay). Herein we present the results of a detailed sediment budget for this river/estuary transitional system. The primary regional goal of the study was to measure sediment transport rates and pathways in the delta in support of ecosystem restoration efforts. In addition to achieving this regional goal, the study has produced general methods to collect, edit, and analyze (including error analysis) sediment transport data at the interface of rivers and estuaries. Estimating sediment budgets for these systems is difficult because of the mixed nature of riverine versus tidal transport processes, the different timescales of transport in fluvial and tidal environments, and the sheer complexity and size of systems such as the Sacramento‐San Joaquin River Delta. Sediment budgets also require error estimates in order to assess whether differences in inflows and outflows, which could be small compared to overall fluxes, are indeed distinguishable from zero. Over the 4 year period of this study, water years 1999‐2002, 6.6 ± 0.9 Mt of sediment entered the delta and 2.2 ± 0.7 Mt exited, resulting in 4.4 ± 1.1 Mt (67 ± 17%) of deposition. The estimated deposition rate corresponding to this mass of sediment compares favorably with measured inorganic sediment accumulation on vegetated wetlands in the delta.