The Columbia River had until recently the world's largest Chinook salmon runs. Restoration of the system's severely decimated runs requires understanding changes in the hydrologic variables (e.g. flow and sediment transport) important to salmonids. We describe here methods to distinguish the human and climate-induced contributions to Columbia River hydrologic processes relevant to the crucial seaward spring migration of juveniles through the tidal river and estuary. Flow regulation has caused most of the decrease in peak flow and sediment transport; it has contributed to changes in spring freshet timing. Climate change has reduced peak and average flows and sediment transport, changing spring-freshet timing by several weeks. Irrigation diversion has reduced the annual average flow as much as climate change. A better understanding of historical changes in hydrologic processes entailed in this paper tells us how management and climate have changed the Columbia River system over time. The separation of the climate and anthropogenic influences used here may assist in policy analyses and strategies aimed at restoration of the Columbia River endangered salmonids, and in management of other systems. Copyright © 2010 John Wiley & Sons, Ltd.