Frequent application of nitrogen fertilizers through irrigation is likely to increase the concentration of nitrate in groundwater. In this study, the HYDRUS-2D/3D model was used to simulate fertilizer movement through the soil under surface (DI) and subsurface drip irrigation (SDI) with 10 and 20 cm emitter depths for tomato growing in three different typical and representative Egyptian soil types, namely sand, loamy sand, and sandy loam. Ammonium, nitrate, phosphorus, and potassium fertilizers were considered during simulation. Laboratory experiments were conducted to estimate the soils’ adsorption behavior. The impact of soil hydraulic properties and fertigation strategies on fertilizer distribution and use efficiency were investigated. Results showed that for DI, the percentage of nitrogen accumulated below the zone of maximum root density was 33%, 28%, and 24% for sand, loamy sand, and sandy loam soil, respectively. For SDI with 10 and 20 cm emitter depths, it was 34%, 29%, and 26%, and 44%, 37%, and 35%, respectively. Results showed that shallow emitter depth produced maximum nitrogen use efficiency varying from 27 to 37%, regardless of fertigation strategy. Therefore, subsurface drip irrigation with a shallow emitter depth is recommended for medium-textured soils. Moreover, the study showed that to reduce potential fertilizer leaching, fertilizers should be added at the beginning of irrigation events for SDI and at the end of irrigation events for DI. As nitrate uptake rate and leaching are affected by soil’s adsorption, it is important to determine the adsorption coefficient for nitrate before planting, as it will help to precisely assign application rates. This will lead to improve nutrient uptake and minimize potential leaching.