The diffusion of autonomous sensing platforms capable of a remote large-scale surveillance of environmental water basins is currently limited by the cost and complexity of standard analytical methods. In order to create a new generation of water analysis systems suitable for continuous monitoring of a large number of sites, novel technical solutions for fluid handling and detection are needed. Here we present a microfluidic device hosting a perfluorinated microporous membrane with refractive index similar to that of water, which enables the combination of filtration and label-free sensing of adsorbing substances, mainly pollutants, in environmental water samples. The cross-flow design of the microfluidic device avoids the clogging of the membrane due to particulate, whereas molecules with some hydrophobic moiety contained in the crossing flow are partially retained and their adhesion on the inner surface of the membrane yields an increase of light scattering intensity, which can be easily measured using a simple instrument based on Light Emitting Diode illumination. By cycling sample water and pure water as a reference, we demonstrate the detection of 0.5 μM of a model cationic surfactant and regeneration of the sensing surface. The optical response of the membrane sensor was characterized using a simple theoretical model that enables to quantify the concentration of target molecules from the amplitude and kinetics of the measured binding curves. The device was tested with real water samples containing large amount of environmental particles, without showing clogging of the membrane, and enabling nonspecific quantification of adsorbing substances in a few minutes.