Safety analysis is of ultimate importance for the operation of Nuclear Power Plants (NPP). Experiments even on a pilot scale are quite expensive and therefore numerical simulations play a major role in this analysis. They allow to predict the behaviour of NPP systems under different operational and accident conditions and to develop proper action plans for minimizing the risks of accidents, and minimizing the consequences of possible accidents. For a proper risk assessment and development of emergency plans, a very large number of scenarios have to be simulated, achieving acceptable accuracy for the critical parameters, such as radioactive pollution and temperature. The existing software tools are either very simplistic and therefore quite inaccurate or they use general CFD codes that makes them very slow. This paper presents a customized algorithm and corresponding software tools for simulation of non-isothermal flows in the containment pool of a NPP. It first summarizes the requirements for such simulation tools and then presents the new algorithm which, in the opinion of the authors, is a proper compromise between accuracy and efficiency for solving such problems. It uses a Fictitious Domain Method (FDM) to impose the boundary conditions, a Cartesian finite volume discretization combined with a Domain Decomposition (DD) technique, and a factorized perturbation of the incompressibility constraint proposed recently in Guermond and Minev (2010). Finally, results from numerical simulations in idealized and realistic geometries are presented and discussed.