Residence time of water flow is an important factor in subsurface media to determine the fate of environmental toxins and the metabolic rates in the ecotone between the surface stream and groundwater. Both numerical and lab-based experimentation can be used to estimate the residence time. However, due to high variability in material composition in subsurface media, a pragmatic model set up in the laboratory to trace particles is strenuous. Nevertheless, the selection and inclusion of input parameters, execution of the simulation, and generation of results as well as post-processing of the outcomes of a simulation take a considerable amount of time. To address these challenges, an automated particle tracing method is developed where the numerical model, i.e., flow and reactive transport code, MIN3P, and MATLAB code for tracing particles in saturated porous media, is used. A rectangular model domain is set up considering a fully saturated subsurface media under steady-state conditions in MIN3P. Streamlines and residence times of the particles are computed with a variety of seeding locations covering the whole model surface. Sensitivity analysis for residence time is performed over the varying spatial discretization and computational time steps. Moreover, a comparative study of the outcomes with Paraview is undertaken to validate the automated model (R2 = 0.997). The outcome of the automated process illustrates that the computed residence times are highly dependent on the accuracy of the integration method, the value of the computational time step, ∆t, spatial discretization, stopping criterion for the integration process of streamlines, location, and amount of seed points. The automated process can be highly beneficial in obtaining insights into subsurface flow dynamics with high variability in the model setup instead of laboratory-based experimentation in a computationally efficient manner.