In this paper, SISO and MIMO robust variable structure controls of fixed bed bioreactors are developed. The process considered must regulate the nitrogen content of drinkable water at desired values imposed by international norms. Micro-organisms fixed in the reactor absorb the nutrients in such a way that the substrate concentrations decrease in the outflowing water. The addition of a carbon source is needed in this operation. A SISO variable structure control is used to regulate only the total concentration of nitrates and nitrites by acting either on the influent flow rate, or on the ethanol concentration. In order to optimise the addition of the ethanol which is the carbon source and regulate the ethanol concentration of drinkable water, a MIMO variable structure control is used. The complexity of a control problem is due to nonlinear and time varying behaviour of micro-organisms used for consuming harmful substrates. The performances of the control laws are illustrated by simulations.