An approach for estimating and controlling biological variables in a continuous flow biological wastewater treatment process is presented and analyzed. The goal in the control is to force the residual substrate and the dissolved oxygen concentrations to track a given reference model despite the disturbances and system parameter uncertainties. The methodology studied is based on direct exploitation of the non linear model representing the wastewater treatment process and is coupled with a joint observer estimator for on line tracking of unavailable states and time varying parameters. The estimated variables are used in the explicit design of the control algorithm according to certainty equivalence principle. A simulation study subject to measurement noise and abrupt jumps in the kinetic parameters shows the feasibility and robustness Of the Control Strategy.