This work presents a methodology which exploits the underlying biochemical structure of bioprocesses to estimate concentrations in aerobic fermenters from oxygen measurements. Although a number of estimators have been proposed over the years in the literature, the methodology proposed in this work is able to operate in transient conditions while does not require the knowledge of the growth kinetics. In addition, it can be also applied to fermenters where the spatial distribution of the concentrations is relevant. In this case, we propose a systematic approach to optimally locate the sensors based on the use of reduced order models. This method allows the reconstruction of the oxygen concentrations from a limited number of sensors. Finally, the methodology proposed will be illustrated on a horizontal tubular reactor for the production of gluconic acid by free-growth of Aspergillus niger.