The growth of microorganisms in a biofilm was monitored, based on available substrate measurements and first principle modeling. The biofilter was described by a set of partial differential equations obtained from species mass balance. Using two interior collocation points, the model was reduced to a set of ordinary differential equations, with sufficient accuracy to describe the growth of biomass along the reactor bed. An extended Kalman filter was designed at three measurement locations, which resulted in an accurate estimation of the process. Simulation results, provided in Mathematica(R) and Matlab(R) environments, showed a significant decrease in the biomass error covariance: 0.0065 to 2.50E-05 and 0.0065 to 1.73E-06 for two different measurement noise levels using a normalized bioreactor length of 0.21. Similar results were obtained at the remaining collocation points. The proposed procedure may have applications for water pollution control.