A two-step methodology is presented for long-term eco-hydrodynamic simulation of a dendritic reservoir that can be subdivided into many interacting subsystems. This approach provides a balance between spatial resolution and simulation time extent. The first step aims at defining the exchange mass and water fluxes among basins. The second step is the eco-hydrodynamic modelling of the subsystems. This methodology is applied to Rapel reservoir, located in central Chile, which can be subdivided into three distinct basins. For this application, a 2D depth-averaged model is used to define exchange fluxes at the basin confluence, while a 1D, horizontally-averaged, vertically resolving model is used to simulate the hydrodynamics and biochemical behaviour of each basin. Dimensional analysis is introduced to analyse the water quality simulations and to determine whether internal processes or external loading are dominant and better explain the measured differences in phytoplankton biomass among the basins. The product of biomass growth rate and basin retention time is identified as an important dimensionless parameter describing the associated dynamics. (C) 2008 Elsevier B.V. All rights reserved.