Historical changes in the hydrology, sedimentology, and physical oceanography of the Columbia River Estuary have been evaluated with a combination of statistical, cartographic, and numerical-modelling techniques. Comparison of data digitized from US Coast and Geodetic Survey bathymetric surveys conducted in the periods 1867-1875, 1926-1937, and 1949-1958 reveals that large changes in the morphology of the estuary have been caused by navigational improvements (jetties, dredged channels, and pile dikes) and by the diking and filling of much of the wetland area. Lesser changes are attributable to natural shoaling and erosion. There has been roughly a 15% decrease in tidal prism and a net accumulation of about 68 × 10 6m 3 of sediment in the estuary. Large volumes of sediment have been eroded from the entrance region and deposited on the continental shelf and in the balance of the estuary, contributing to formation of new land. The bathymetric data indicate that, ignoring erosion at the entrance, 370 to 485 × 10 6m 3 of sediment has been deposited in the estuary since 1868 at an average rate of about 0.5 cm y -1, roughly 5 times the rate at which sea level has fallen locally since the turn of the century. Riverflow data indicate that the seasonal flow cycle of the Columbia River has been significantly altered by regulation and diversion of water for irrigation. The greatest changes have occurred in the last thirty years. Flow variability over periods greater than a month has been significantly damped and the net discharge has been slightly reduced. These changes in riverflow are too recent to be reflected in the available in the available bathymetric data. Results from a laterally averaged, multiple-channel, two-dimensional numerical flow model (described in HAMILTON, 1990) suggest that the changes in morphology and riverflow have reduced mixing, increased stratification, altered the response to fortnightly (neap-spring) changes in tidal forcing, and decreased the salinity intrusion length and the transport of salt into the estuary. The overall effects of human intervention in the physical processes of the Columbia River Estuary (i.e. decrease in freshwater inflow, tidal prism, and mixing; increase in flushing time and fine sediment deposition, and net accumulation of sediment) are qualitatively similar to those observed in less energetic and more obviously altered estuarine systems. A concurrent reduction in wetland habitats has resulted in an estimated 82% reduction in emergent plant production and a 15% reduction in benthic macroalgae production, a combined production loss of 51,675 metric tons of organic carbon per year. This has been at least partially compensated by a large increase in the supply of riverine detritus derived from freshwater phytoplankton primary production. Comparison of modern and estimated preregulation organic carbon budgets for the estuary indicates a shift from a food web based on comparatively refractory macrodetritus derived from emergent vegetation to one involving more labile microdetritus derived from allochthonous phytoplankton. The shift has been driven by human-induced changes to the physical environment of the estuary. While this is a relatively comprehensive study of historical physical changes, it is incomplete in that the sediment budget is still uncertain. More precise quantification of the modern estuarine sediment budget will require both a better understanding of the fluvial input and dredging export terms and a sediment tranport model designed to explain historical changes in the sediment budget. Oceanographic studies to better determine the mechanisms leading to the formation of the turbidity maximum are also needed. The combination of cartography and modelling used in this study should be applicable in other systems where large changes in morphology have occurred in historical time.