We monitored California Sea Lions (Zalophus californianus) in the lower Columbia River Basin from 1997 to 2018 to document their seasonal and annual occurrence in the estuary and to determine what fraction of that population was preying on salmonids (Oncorhynchus spp.) at Bonneville Dam on the Columbia River or Willamette Falls on the Willamette River. Based on periodic haul-out counts at the South Jetty (river km 0) and the East Mooring Basin (river km 25), we found that since 1999, several thousand California Sea Lions regularly hauled out at the mouth of the river, particularly during autumn months, but similar numbers did not occur inside the estuary until 2013, and then primarily during spring months. Haul-out use of the East Mooring Basin followed a bimodal pattern, with peaks during autumn (northward migration) and spring (southward migration), and troughs during summer (breeding season) and winter. Based on trapping and branding 2651 California Sea Lions at the East Mooring Basin through 2016, and brand resights at Bonneville Dam (river km 235) and Willamette Falls (river km 206) through 2017, we found that only 6.5% of the sea lions in the estuary recruited into the population of upriver “problem” animals that preyed on threatened and endangered salmonids. Besides documenting long-term abundance and movement patterns of sea lions, our monitoring program served as a research platform for other scientists and provided the foundation for California Sea Lion management policy in the Columbia River Basin.