Fine particle deposition within riverbeds plays a major role in riverine ecology and biogeochemistry by altering hyporheic exchange flux. Moreover, it is ubiquitous within streams and rivers across all flow stages. However, the dynamics of fine particle deposition are still not completely understood in rivers, and continuum models like the advection dispersion equation require modifications to represent the processes accurately. To enhance understanding of fine particle dynamics, we developed a novel numerical particle tracking model that simulates fine particle deposition as a stochastic process under losing, neutral, and gaining streamflow conditions. These flow conditions generate three different velocity profiles by combining the free surface and groundwater flows. In addition, a novel aspect of our model is the storage of filtered particles to estimate concentration fields within the bed. Our simulated results are qualitatively compared with previous laboratory flume experimental results of kaolinite deposition under similar conditions. The model indicates that fine particle deposition patterns and residence time functions depend heavily on the exchange flux between stream and groundwater, as well as bed filtration properties as the deposition of particles occurs at greater depths in the losing stream condition than in the neutral and gaining cases. Therefore, the spatial pattern of particle deposition is a direct result of pore water velocity profiles, while the concentration depends on filtration dynamics within the bed.