This study reports on the use of dynamic simulation for wastewater treatment units involving submerged packed biofilters. It enlights different aspects of the dynamic modelling of such non conventional systems (biological reaction scheme, ...) and the numerical strategy used to solve the resulting set of Partial Differential Algebraic equations (PDAE). Illustrative applications in the case of denitrification and denitritation with pilot plant data comparison sketch the interest of dynamic simulation.