Water and wastewater processing (cooling tower, heat exchanger, treatment, etc.) generate desirable or undesirable biofouling (mineral, organic, biological) which may affect equipment or process performances. Fouling magnitude and nature stand as critical parameters to be evaluated in-situ and on-line to control and optimize the operation (production, cleaning). A fouling sensor based on a Micro-Electro-Mechanical Systems (MEMS) structure generating a local in-situ periodic thermal excitation (PTR) was studied in order to quantify and qualify fouling. At lab scale, model deposit (PVC) were used to simulate fouling conditions. Limits of detection (LOD) and quantification (LOQ) under steady and periodic thermal regimes were compared. Transposition to industrial conditions was investigated at pilot plant scale. A continuous bioprocess (PropellaTM reactor) was fed with diluted wastewater under controlled operating condition (temperature, mixing rate, flow rates, residence time) in order to mimic realistic industrial conditions and to generate a complex biofouling over six weeks. Thermal diffusivity, capacitive and resistive components are extracted from thermal spectrum response and a final fouling factor is introduced. Results demonstrate the ability to quantify and qualify a complex biofouling with in-situ and on-line information.