We address restoration of eutrophic lakes and reservoirs through the formulation of dynamic optimization problems subject to complex PDAE systems representing biogeochemical processes in the water bodies. The model includes phytoplankton, zooplankton, fish, nutrients, DO, particulate and dissolved carbon dynamics. The PDAE has been transformed into an ordinary differential algebraic equation system by spatial discretization into two water layers. An optimal control problem for the implementation of three different restoration techniques and their combinations has been formulated within a control vector parameterization approach. Numerical results for the different problems provide optimal profiles for tributary deviation flowrate through a nearby wetland, aeration rates and fish removal rates, as restoration strategies. (C) 2011 Elsevier Ltd. All rights reserved.