Individuals of different interacting populations often adjust to prevailing conditions by changing their behavior simultaneously, with consequences for trophic relationships throughout the system. While we now have a good theoretical understanding of how individuals adjust their behavior, the population dynamical consequences of co-adaptive behaviors are rarely described. Further, mechanistic descriptions of ecosystem functions are based on population models that seldom take behavior into account. Here, we present a model that combines the population dynamics and adaptive behavior of organisms of two populations simultaneously. We explore how the Nash equilibrium of a system - i.e. the optimal behavior of its constituent organisms - can shape population dynamics, and conversely how population dynamics impact the Nash equilibrium of the system. We illustrate this for the case of diel vertical migration (DVM), the daily movement of marine organisms between food-depleted but safe dark depths and more risky nutrition-rich surface waters. DVM represents the archetypal example of populations choosing between a foraging arena (the upper sunlit ocean) and a refuge (the dark depths). We show that population sizes at equilibrium are significantly different if organisms can adapt their behavior, and that optimal DVM behaviors within the community vary significantly if population dynamics are considered. As a consequence, ecosystem function estimates such as trophic transfer efficiency and vertical carbon export differ greatly when fitness seeking behavior is included. Ignoring the role of behavior in multi-trophic population modeling can potentially lead to inaccurate predictions of population biomasses and ecosystem functions.