Bacterial contamination of water sources (e.g., lakes, rivers and springs) from waterborne bacteria is a crucial water safety issue and its prevention is of the utmost significance since it threatens the health and well-being of wildlife, livestock, and human populations and can lead to serious illness and even death. Rapid and multiplexed measurement of such waterborne pathogens is vital and the challenge is to instantly detect in these liquid samples different types of pathogens with high sensitivity and specificity. In this work, we propose a biosensing system in which the bacteria are labelled with streptavidin coated magnetic markers (MPs—magnetic particles) forming compounds (MLBs—magnetically labelled bacteria). Video microscopy in combination with a particle tracking software are used for their detection and quantification. When the liquid containing the MLBs is introduced into the developed, microfluidic platform, the MLBs are accelerated towards the outlet by means of a magnetic field gradient generated by integrated microconductors, which are sequentially switched ON and OFF by a microcontroller. The velocities of the MLBs and that of reference MPs, suspended in the same liquid in a parallel reference microfluidic channel, are calculated and compared in real time by a digital camera mounted on a conventional optical microscope in combination with a particle trajectory tracking software. The MLBs will be slower than the reference MPs due to the enhanced Stokes’ drag force exerted on them, resulting from their greater volume and altered hydrodynamic shape. The results of the investigation showed that the parameters obtained from this method emerged as reliable predictors for E. coli concentrations.