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The Trinity River Restoration Program implements a variety of rehabilitation actions on the Trinity River downstream from Lewiston Dam. These actions, which include mechanical channel reconfiguration, gravel additions, and high-flow releases from Lewiston Dam, have the potential to affect the depth and morphology of the stream. Local stakeholders have expressed concern that some of these activities could result in the filling of some of the deep pools used as holding habitat by adult salmonids. This report documents the results of an assessment of whether widespread changes in pool depths are indeed occurring, and if so, where and why they are occurring. Depth changes are evaluated over two different time periods: Recent changes in pool geometry are assessed by comparing bed elevations acquired at 139 locations with sonar in 2009, 2010, and 2011, whereas depth changes spanning multiple decades at 13 locations are evaluated with a review of historical records. Result of the recent sonar measurements indicates that the depths of most pools and deep runs increased between 2009 and 2011. Of 139 locations considered in this study, slightly more than half increased in depth over the study period. Significant depth decreases were observed in relatively few locations. In many cases, however, those decreases appear to be linked to recent rehabilitation actions. In particular, terrace lowering at channel rehabilitation projects sites was found to be associated with moderate to large depth decreases in about 12 distinct pool locations. Gravel additions alone, on the other hand, appear to have relatively little impact on pool depths. Of nine pools located within a few channel widths downstream from gravel additions but not adjacent to an area of terrace lowering, depth decreases were observed in just two locations. Neither terrace lowering nor gravel addition appears to have much effect on pool depths in more remote downstream reaches. A review of historical pool depth data indicates that the combination of higher flow releases from Lewiston Dam and reduced delivery of fine sediment from tributary watersheds has resulted in an increase in the depths of most natural pools in the Trinity River since the mid-20th Century.