Habitat Monitoring on the San Juan River

The San Juan River Basin Recovery Implementation Program (Recovery Program) was established in 1991 to allow water development to continue within the Basin while still complying with the Endangered Species Act and protecting the endangered Colorado pikeminnow and razorback sucker. The Recovery Program consists of partners who are committed to the recovery of the listed fishes under the Endangered Species Act and includes water users, conservation groups, state, federal and tribal agencies. For further information on the Recovery Program, see https://coloradoriverrecovery.org/sj/. The San Juan River is partially regulated by Navajo Dam. There are several tributaries that flow into the San Juan River between the dam and Lake Powell, but substantial diversions occur from these tributaries limiting the contribution to the flow regime. Operation of Navajo Dam began in 1962 and has resulted in altered flow into the San Juan River with a tendency towards reduced spring flows in some years and supplemented flows in other seasons. Because frequency and magnitudes of flows are important triggers for various life cycle stages of endangered species, the Recovery Program developed flow recommendations to guide releases from Navajo Dam. The flow recommendations are designed to meet the conditions required to develop and maintain habitat for Colorado pikeminnow and razorback sucker and provide the necessary hydrologic conditions for the various life stages of endangered and other native fishes. The habitat monitoring that is part of this project will be used to evaluate the effectiveness of flow recommendations and management actions on habitat. Since 1992, aerial imagery has been collected along the San Juan River between the confluence of the Animas River (River Mile (RM) 180) and the inflow of Lake Powell (the interface between the San Juan River and Lake Powell) to as far downriver as Neskahi Canyon (RM -30). A light detection and ranging (LiDAR) flight was conducted in 2013. The imagery is used within the Recovery Program to track changes in channel morphology and habitat. Specifically, the number and area of low velocity habitat (backwaters, Notice of Funding Opportunity No. R24AS00327 2 embayments), total wetted area (wetted habitat and wetted channels of the river), and island complexes (used as a surrogate for habitat complexity) are quantified (Table 1). This extensive data set allows for tracking changes in habitat and assessing the effectiveness of management actions, implemented flows, and intra- and inter-annual variability in flows. The last analysis was conducted in 2022.