Abstract. We describe some features of a three-dimensional numerical simulator currently under development for studying water physico-chemical properties during the flooding of hydroelectric plants reservoirs. The work is sponsored by the Brazilian Electric Energy National Agency (ANEEL) and conducted with Furnas Centrais Elétricas S. A., the leading Brazilian power utility company. An overview of the simulator requirements is given. The mathematical model, the software modules, and engineering solutions are briefly discussed, including the finite element based transport module. We compare methods, iterative methods and preconditioners used to solve the sparse linear systems which arise from the discretization of three-dimensional partial differential equations.