7703

• UCREFRP Catalog Number: 7703
• Author: Pucherelli, M. J. and W. P. Goettlicher.
• Title: Mapping an Instream Habitat on the San Juan River Using Airborne Videography.
• USFW Year: 1992.
• USFW - Doc Type: Washington, D.C.
• Copyright Material: NO

INTRODUCTION

The Animas/LaPlata is a water development project (Project) in southern Colorado and
northern New Mexico in the San Juan River Basin. The Project was authorized by the Colorado
River Basin Project Act of September 30, 1968, as a participating project under the Colorado
River Storage Act of April 11, 1956. Subsequent authorization for the construction,
maintenance, and operation of the Project was granted under the Colorado River Basin Act and
the Colorado Ute Indian Water Rights settlement of 1988. However, concern over the impact of
water depletions by the Project on endangered species resulted in a Jeopardy Opinion under the
ESA (Endangered Species Act) by the U.S. Fish and Wildlife Service (Service). Subsequently, a
Reasonable and Prudent Alternative was crafted which allowed the Project to proceed providing
that a multiyear research plan was developed and implemented, depletions were limited until
results of the research could be obtained, and Navajo Dam operated to produce test flows
mimicking a natural hydrograph. In addition, in July 1991 the U.S. Bureau of Reclamation
(Reclamation) requested consultation under the ESA on the operation of Navajo Dam and
agreed to release test flows during the 7-year research period so that flow effects on the
endangered fish and other native and non-native fishes below Navajo Dam could be determined.

This study is part of an interdisciplinary research effort addressing biological, hydrologic, and
sediment issues. This study, using videographic techniques, assesses flow levels in the San
Juan River versus habitat quantity (main channel and low velocity habitats such as backwaters
and side channels) needed for several life stages of the native fish. Studies conducted by the
Service concluded that backwaters in the Green River are preferred habitat for YOY
(young-of-the-year) Colorado squawfish (Holden and Stalnaker, 1975; Holden, 1977; Tyus and
McAda, 1984; Tyus et aI., 1987). Squawfish spawn during mid to late summer and their larvae
become distributed in shallow backwater habitat, reducing predation and protecting them from
adverse flow events (Tyus et al., 1987). This evidence suggests that maximizing backwater
habitat during summer will increase the survival rate of young Colorado squawfish and,
therefore, would be an important factor in the management and preservation of the species.
Studies conducted by Pucherelli et al., 1990a and 1990b, document backwaters per river mile in
the San Juan River to be three times less than backwaters in the Green River. This evidence
suggests that squawfish may be using the more available side channel habitat as well as
backwaters.

A technique was required to accurately map backwater habitat in response to various San Juan
River flows. The IFIM (instream flow incremental method) has not proven adequate to calculate
backwaters on large turbid and hydrologically complex rivers such as the Green River (Rose
and Hann, 1989). Rose and Hann's finding would apply to the San Juan because of similar
conditions. Therefore, alternative methods were employed. Pucherelli et al., 1990a, 1990b, and
1987, used aerial photographs and a GIS (Geographic Information System) to map backwater
habitat and changes in river morphology as a function ofriverflow.

This study examines the pretest flow operation relationship between flow and the number and
area of backwaters and side channels on the San Juan River in New Mexico and Utah. The
objective is to collect several years of habitat data from different flow scenarios and establish a
data base to assist in determining the optimal San Juan River flows needed to maximize low

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