In this paper, we present a method for detecting and quantifying pathogens in water samples. The method proposes a portable dark field imaging and analysis system for quantifying E. coli concentrations in water after being labeled with magnetic particles. The system utilizes the tracking of moving micro/nano objects close to or below the optical resolution limit confined in small sample volumes (~ 10 μl). In particular, the system analyzes the effect of volumetric changes due to bacteria conjugation to magnetic microparticles (MP) on their Brownian motion while being suspended in liquid buffer solution. The method allows for a simple inexpensive implementation and the possibility to be used as point-of-need testing system. Indeed, a working prototype is demonstrated with the capacity of quantifying E. coli colony forming units (CFU) at a range of 1x10³ - 6x10³ CFU/mL.