The life cycle of several sessile or highly sedentary aquatic species is characterized by a pelagic stage, during which propagules are dispersed by the water flow. As a consequence, hydrodynamics plays a crucial role in redistributing offspring. In this work, we describe an integrated modeling framework that couples a minimal – yet biologically well founded – ecological model for the population dynamics at the local scale to an efficient numerical model of three dimensional free surface flows in a thermally forced basin. The computed hydrodynamical fields are employed in a Lagrangian description of larval transport at the basin scale. The developed modeling framework has been applied to a realistic case study, namely the spread of an idealized aquatic sedentary population in Lake Garda, Italy. The analysis of this case study shows that the long-term interplay between demography and hydrodynamics can produce complex spatiotemporal dynamics. Our results also evidence that larvae can travel over relatively long distances even in a closed basin. A sensitivity analysis of the model outcomes shows that both biological traits and external forcings may remarkably influence the evolution of diffusion patterns in space and time.