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Concerns have been raised over the potential impacts of the Animas/LaPlata project and the regulation of Navajo Dam. Flow depletions in the San Juan River may adversely affect the remnant population of the native fish, particularly the endangered Colorado squawfish and the razorback sucker. A multiyear research program is currently being conducted on the San Juan River as a result of a Jeopardy Opinion delivered by the U.S. Fish and Wildlife Service on Animas/LaPlata and the subsequent Reasonable and Prudent Alternative that was accepted. A mulidisciplinary research team composed of representatives from the affected agencies is currently investigating the relationship between flow and survival of native fish species in the San Juan. This study explores the relationship between flow and important native fish habitats on the San Juan River in New Mexico and Utah. Specifically, it examines the number and area of backwaters and side channels and their relationship to flow levels. Airborne videography is used for this study instead of more expensive aerial photography. The data suggest strong relationships between flow and backwater and side channel area. Backwater area was maximized at the lowest flows and side channel area was maximized at peak flow.