Industrially applied bioelectrochemical systems require long-term stable operation, and hence the control of biofilm accumulation on the electrodes. An optimized application of biofilm control mechanisms presupposes on-line, in-situ monitoring of the accumulated biofilm. Heat transfer sensors have successfully been integrated into industrial systems for on-line, non-invasive monitoring of biofilms. In this study, a mathematical model for the description of the sensitivity of a heat transfer biofilm sensor was developed, incorporating the hydrodynamic conditions of the fluid and the geometrical properties of the substratum. This model was experimentally validated at different flow velocities by integrating biofilm sensors into cylindrical pipes and planar mesofluidic flow cells with a carbonaceous substratum. Dimensionless sensor readings were correlated with the mean biovolume measured gravimetrically, and optical coherence tomography was used to determine the sensors' sensitivity. The biofilm sensors applied in the planar flow cells revealed an increase in sensitivity by a factor of 6 compared to standard stainless steel pipes, as well as improved sensitivity at higher flow velocities.