Quantification methods of mass transport of contaminants such as nitrate into groundwater are still inefficient due to lack of knowledge about the parameters governing the transport process. Thus, in this research, a new methodology called optimized diffusion cell (ODC) setup was established to investigate nitrate input into groundwater through an unsaturated zone. This experimental modeling setup mimics the emission-transmission-immission (ETI) concept, which allows for quantification of input and output nitrate fluxes under realistic conditions. Three various nitrate concentrations were added to undisturbed soil samples of 1 cm thickness. The ODC setup was established to minimize the advective transport of nitrate in sandy soil samples due to high permeability. Outcomes revealed that a sorbed amount of nitrate was little due to advective transport compared to that carried out by diffusion. Additionally, for the whole analyzed soil samples of different soil classes, the amount of sorbed nitrate by advection did not exceed 1% of the total sorbed amount. On average, 30% of total nitrate mass input was sorbed. Results of the ODC setup prove its efficiency to simulate nitrate mass transport within the enclosed soil samples. Such findings can be used to predict endurable risk of nitrate transport to groundwater and to analyze sorption isotherms.