Monitoring of the biological degradation of a substrate by microorganisms is a key issue, especially in the soil bioremediation area. Respiration measurement is the easiest way to obtain online information on the biological activity. Nevertheless, it is indirectly related to substrate consumption and microbial growth. To be able to link these phenomena, a robust and descriptive model has been developed. Both biological and gas/liquid transfer dynamics must be taken into account to link the online measurement with the actual biological respiration. For that, experimental evolution of the respiratory ouotient (RQ) during a biodegradation has been compared against general biodegradation knowledge. To obtain a reliable model, practical and structural sensitivity analyses have been conducted. The model can describe the evolution of both online measurable and non-measurable states. It also gives a new definition of the apparent RQ, measured in the gas phase, compared to the actual biological RQ.