This paper discusses mathematical model implementations and simulation in various software environments for Unmanned Underwater Vehicles (UUVs), especially biomimetic ones. Gaining accurate simulation models of UUVs is challenging due to many nonlinear phenomena that need to be analysed. Further, the sensors’ accuracy and disturbances made by the natural water environment are difficult to predict during the simulation. On the other hand, an accurate simulation model is needed during new algorithm tests provided for increased vehicle autonomy. As a result, mathematical models and their implementation into different software are analysed and discussed in this paper. The model based on nonlinear differential equations is compared to an object-oriented, physical model based on Matlab Simscape Multibody.