SummaryThe purpose of this document is to describe research, monitoring, and evaluation (RME) for the Federal Columbia River Estuary Program, hereafter called "the Estuary Program." The intent of this RME effort is to provide data and information to evaluate progress toward meeting program goals and objectives and support decision making in the Estuary Program. The goal of the Estuary Program is to understand, conserve, and restore the estuary ecosystem to improve the performance a of listed salmonid populations. The Estuary Program has five general objectives, designed to fulfill the program goal, as follows.1. Understand the primary stressors affecting ecosystem controlling factors, such as ocean conditions and invasive species. 2. Conserve and restore factors controlling ecosystem structures and processes, such as hydrodynamics and water quality. 3. Increase the quantity and quality of ecosystem structures, i.e., habitats, juvenile salmonids use during migration through the estuary. 4. Maintain the food web to benefit salmonid performance. 5. Improve salmonid performance in terms of life history diversity, foraging success, growth, and survival.The goal of estuary RME is to provide pertinent and timely research and monitoring information to planners, implementers, and managers of the Estuary Program. The goal leads to three primary management questions pertaining to the main focus of the Estuary Program: estuary habitat conservation and restoration. 1) Are the estuary habitat actions achieving the expected biological and environmental performance targets? 2) Are the offsite habitat actions in the estuary improving juvenile salmonid performance and which actions are most effective at addressing the limiting factors preventing achievement of habitat, fish, or wildlife performance objectives? 3) What are the limiting factors or threats in the estuary/ocean preventing the achievement of desired habitat or fish performance objectives?Performance measures for the estuary are monitored indicators that reflect the status of habitat conditions and fish performance, e.g., habitat connectivity, survival, and life history diversity. Performance measures also pertain to implementation and compliance. Such measures are part of the monitoring, research, and action plans in this estuary RME document. Performance targets specific to the estuary were not included in the 2007 draft Biological Opinion.To address the estuary RME goal and management questions, estuary RME has the following objectives and associated sub-objectives: a Salmonid performance means life history diversity, foraging success, spatial structure, and growth . AER 3. Develop and implement a methodology to estimate the cumulative effects of habitat conservation and restoration projects in terms of cause-and-effect relationships between ecosystem a Status and trends monitoring is defined as census or statistically designed monitoring of fish or wildlife populations and/or environmental conditions (i.e., watershed conditions) to assess the current status (at a p...