The reconstruction is addressed of the dynamics of the microbial oxygen uptake rate (OUR) and carbon dioxide evolution rate (CER) from off-gas concentration measurements and dissolved oxygen measurements during highly dynamic conditions, encountered, for example, during a substrate-pulse experiment. The reconstruction of the OUR and CER is done by fitting a model for the mass transport to the measured data using smoothing techniques. Most of the parameters of the mass-transport model, including the sensor dynamics, are derived from physical knowledge. A few remaining parameters that cannot be derived from physical knowledge are computed by fitting the model to an identification data set. It is demonstrated that the net gas production or consumption can have a significant impact on the estimated OUR, and, therefore, is included in the model. Besides the reconstruction of the OUR and the CER, the reconstruction algorithm also incorporates the monitoring of the mass-transfer coefficient kla.