Hydropower reservoirs impounded by high-head dams exhibit complex circulation which confuses the downstream migrating salmon and limits successful collection and passage of fish. Fish passage engineers attempt to modify the hydrothermal behavior at reservoirs through structural and operational modifications and often use hydrodynamic simulations to guide their actions. Simulation of key hydrothermal processes such as (a) development of a stable 2-layer stratified system, (b) density driven currents over a reservoir length scale, and (c) discharge hydraulics near the power generation and fish collection intakes, requires highly specialized models applied at differing temporal and spatial scales. A staged modeling approach is presented which uses external coupling of models at varying temporal scales and spatial resolution to simulate the entire hydraulic regime from the mouth of the reservoir at the upstream end to the discharge at the dam. The staged modeling approach is illustrated using a case study where structural modifications were evaluated to improve reservoir stratification and density driven currents. The model results provided input and valuable insight in the development of a new structure design and configuration for effective fish collection near the forebay of a high head dam.