The article deals with modeling of a system with hybrid dynamics and with two tools for modeling of such systems. For purpose of modeling we chose the system of coupled tanks. The tanks are situated in different heights and dynamics of the system changes in the moment when the liquid level in the second tank runs over the height of bottom of the first tank. That represents hybrid nature of this system. We chose two tools for simulation of hybrid systems - MPT toolbox and HYSDEL and we specifically aim on modeling of the system of coupled tanks by both these tools and on comparison of these tools. The tools are free however they do not work independently but as a part of the simulation language Matlab.