A dynamic habitat and population model has been developed and applied to the tailwater below Glen Canyon Dam to estimate the dam operation’s effects on rainbow trout (Oncorhynchus mykiss) habitat and population dynamics. Water depth, flow temperature, flow velocity, and substrate types were used as the suitability parameters and to evaluate these indicators. Historic hydraulic data from 1991 to 2009 were analyzed to determine the minimum, mean, and maximum flow rates that were used to represent the habitat suitability index (HSI) and overall suitability index (OSI) of the rainbow trout fry, adult, and spawning life stages, respectively. Fish abundance and the simulation results were also compared with observed fish numbers. Results indicated that under the historic dam operation, the habitat suitability level in the Colorado River was not suitable for fry and spawning rainbow trout, but very suitable for adult rainbow trout. It is indicated that high HSI levels do not mean high fish abundance. It can also be seen that overall rainbow trout abundance decreased during the period 1991 to 2009.