Health of the population of rainbow trout Oncorhynchus mykiss in the San Juan River tailwater was monitored to determine the effects of potential crowding from a reduced winter flow test at Navajo Dam, northwestern New Mexico. A systematic necropsy-based health profile provided a rapid method to detect gross changes in the health of the fish population. The health assessment index (HAI) was calculated to quantify the necropsy system and allow statistical comparisons of data sets. Other suborganismic indices were selected to encompass a range of responses specific to the stress of environmental alterations: physiology assessment using total protein and percent muscle lipids, an immune assessment using serum lysozyme, and a cellular-based evaluation using histology. The HAI values showed no clear trend in fish health, although significant differences occurred among fish samples during the test. Significant declines in condition factors and percent muscle lipids throughout the study suggested a seasonal effect. Total protein and lysozyme levels were variable, showing no discernible patterns. Most histological observations appeared to be incidental during the study. Although there was no clear demonstrable effect of altered flow on fish health, this study revealed the sensitivities of various health indicators, which may help in designing future studies and supporting or interpreting results using these approaches.