Negative interactions of Rainbow Trout Oncorhynchus mykiss with endangered Humpback Chub Gila cypha pose challenges to the operation of Glen Canyon Dam (GCD) to manage for both species in the Colorado River. Operations to enhance the Rainbow Trout tailwater fishery may lead to an increase in downstream movement of the trout to areas where they are likely to interact with Humpback Chub. We evaluated the effects of dam operations on age-0 Rainbow Trout in the tailwater fishery to inform managers about how GCD operations could benefit a tailwater fishery for Rainbow Trout; although this could affect a Humpback Chub population farther downstream. A near year-long increase in discharge at GCD in 2011 enabled us to evaluate whether high and stable flows led to increased spawning and production of age-0 Rainbow Trout compared with other years. Rainbow Trout spawning was monitored by fitting a model to observed redd counts to estimate the number of redds created over a spawning season. Data collected during electrofishing trips in July–September and November were used to acquire age-0 trout population and mortality rate estimates. We found that high and stable flows in 2011 resulted in 3,062 redds (1.7 times the mean of all survey years) and a population estimate of 686,000 age-0 Rainbow Trout (second highest on record). Despite high initial abundance, mortality remained low through the year (0.0043%/d) resulting in significant recruitment with a record high November population estimate of 214,000 age-0 Rainbow Trout. Recent monitoring indicates this recruitment event was followed by an increase in downstream migration, which may lead to increased interactions with downstream populations of Humpback Chub. Consequently, while our results indicate that manipulating flow at GCD can be used to manage Rainbow Trout spawning and recruitment, fisheries managers should use flow manipulation in moderation to minimize downstream migration in order to reduce negative interactions with other species in the Colorado River.