The motion of particles plays an essential role in flow visualization and quantification. In the recent years, particle and colloid tracing in saturated and unsaturated porous media have been widely studied in various applications. Nano- and micro-seeding particles are introduced into a flow to record their motion and subsequently estimate the kinematics of fluids flow. This, by means of many techniques, would allow exploring the fluids flow behavior in plenty of applications in various fields of studies (e.g., Underground-water management and treatment, manage and engineer underground environmental contaminants, Enhanced Oil Recovery). In this work, we apply an experimental technique with the assistance of an image processing and analysis software (ImageJ-2/ Fiji®), and a matrix-based programming language (MATLAB®) to computationally analyze and visualize the fluid flow in porous media. We used microfluidic systems with representative porous structures to define the trajectories (flow lines) of neutrally buoyant micro-polystyrene particles (10-µm diameter), flowing in two-dimensional, water-saturated, microporous networks. By visually tracking individual particles across the micromodel, measuring their average residence time, and comparing it with the estimated saturating-fluid’s residence time, we were able to observe the particle dispersion and breakthrough behavior, as well as their microscopic preferential flow paths. Moreover, tracing particles in a realistic micromodel enabled us to measure the particles instantaneous and average interstitial velocities in porous structures at different flow rates. The resulting data was used to quantify the microscopic flow field and to prove the existence of preferential pathways. In this thesis, the developed particle tracing technique to quantify the velocity field at the pore scale, is thoroughly discussed and documented. This includes the conventional and fluorescence microscopic images acquisition, processing, and analyzing procedures; the designed combination between the Particle Tracker 2D/3D plugin of Image-J2/Fiji® tool, and the MATLAB® language; as well as the developed MATLAB® code for the calculation and visualization of the velocity field’s vectors and magnitudes.‬‬‬‬ Finally, as the outlook of this work, we applied this method to compare the preferential flow paths in a water-saturated medium with a pre-established biomass system. This is expected to give a better understanding of the effects of biomasses accumulation on the flow properties.