In highly regulated systems, like large dammed rivers, conservation legislation requires that systems are managed, in part, to avoid adverse impacts on endangered species. However, multiple endangered species can occur in the same system, and management actions that benefit one species may be detrimental to another species. The current water management strategies in the Sacramento River basin are an example of this conflict. Cold-water releases from Shasta Reservoir during the summer and fall months are aimed at protecting Sacramento River winter-run Chinook (SRWRC) salmon by providing suitable incubation temperatures for their eggs. However, the effects of these regulated water temperature releases on another threatened species, green sturgeon, are less well understood. In this study, we applied a simplified dynamic energy budget (DEB) model (aka DEBkiss) to explore the effect of food limitation and water temperature on the growth rates of green sturgeon. This model captures these effects and able to predict the growth of green sturgeon at different food levels and temperature conditions. We then linked the DEB model with a physically‐based water temperature model. We applied the DEB - water temperature linked model for green sturgeon along with a temperature-dependent egg to fry survival model for SRWRC salmon to quantify the consequences of managing water temperatures to improve salmon eggs survival on the growth rate of green sturgeon. We found that mean temperature-dependent egg-to-fry survival of salmon increased across a modeled environmental gradient from critically dry to wet water year types, while the fractional growth rate of juvenile green sturgeon showed the opposite trend, and decreased as water years transitioned from dry to wet conditions. We also found a non-linear negative correlation between temperature-dependent mean growth rate of green sturgeon and mean temperature-dependent egg-to-fry survival of salmon, which indicated there is a river temperature related trade-off between early growth rate of green sturgeon and embryonic stage survival of salmon. However, the relatively small gains in the growth rate of green sturgeon achieved in years when temperature criteria for SRWRC salmon eggs were not met came at the cost of large reduction in temperature-dependent egg-to-fry survival of salmon. Thus, we concluded the current Sacramento River water-temperature management for the eggs of the endangered SRWRC salmon eggs have a relatively small impact on the growth rate of green sturgeon.