Analysis of field data and development and application of a dynamic model indicate that the processes that control the number and distribution of age-0 Colorado pikeminnow in the middle Green River are poorly understood. Colorado pikeminnow are a federally endangered species endemic to the Colorado River basin that utilize backwaters during their larval stage. The present agency-mandated field sampling program for backwater habitats may be inadequate because it takes place at a time when the model predicts that most larval fish have drifted beyond the study area. The model predicts that water releases from Flaming Gorge Dam have a large potential effect on larval drift, because high releases at the time of drift greatly increase the proportion of the population transported beyond the study area to unfavorable river environments. Development of the model shows that the role of the geomorphic and hydraulic attributes that control larval drift and transport into backwaters, and that were parameterized in the model, are not well known. Resolution of these uncertainties by field study and experimentation would lead to refining this river management tool.