This report describes the water-quality data collected by the USGS from 2004 through 05 as part of the Ecosystem Monitoring Project and attempts to quantify the spatial distribution and temporal variation of water-quality conditions, including contaminant concentrations, in water and suspended sediment in the Columbia River Estuary, and evaluate these water-quality conditions against aquatic-life standards and guidelines. The analytes to be measured in this study were selected because they are either known to be present in Columbia River salmonids at levels of concern; known to be present in salmonids, but not known if present at levels of concern; present in water at concentrations known to affect endocrine function in adult salmonids; or not previously measured in water, but if present, are of potential concern to salmonid populations.