The aim of this work is to estimate and control a biological nitrogen removal process. The paper illustrates the use of a complex nonlinear model in the design of a software sensor and a non linear predictive control technique based on a phenomenalogical model of the process. This model describes the complete dynamics of autotrophic and heterotrophic biomasses, biodegradable organic and nitrogenous matters. The control approach structure is combined with the Kalman Filter, for the on-line reconstruction of unmeasured biological states and unknown parameters of the bioprocess. The efficiency of both the control and estimation are demonstrated via computer simulations.