Plastic mulch in combination with drip irrigation present a common agricultural management technique practiced in commercial vegetable production. This management can result in various impacts on water and nutrient distribution and consequently affect nutrient dynamics in underlying soil. The aim of this work was to: (i) compare the effects of different mulching types (color) on soil temperature and (ii) crop growth; (iii) estimate the effect of plastic mulch cover (MULCH) on water and (iv) nitrate dynamics using HYDRUS-2D. The field experiment was designed in the Croatian coastal karst area on main plots with three levels of nitrogen fertilizer: 70, 140, and 210 kg ha−1, which were all divided in five subplots considering mulch covering with different colors types (black, brown, silver, and white) and no covering (control). Monitoring of water and nitrate dynamics was performed through lysimeters which ensured input data for HYDRUS-2D model. The experimental results showed that plastic mulch had a significant effect on soil temperature regime and crop yield. The dark color mulch (black, brown) caused higher soil temperature, which consequently enabled earlier plant development and higher yields. HYDRUS-2D simulated results showed good fitting to the field data in cumulative water and also nitrate outflow. Water flow simulations produced model efficiency of 0.84 for control (CONT) and 0.56 for MULCH systems, while nitrate simulations showed model efficiency ranging from 0.67 to 0.83 and from 0.70 to 0.93, respectively. Additional simulations exposed faster transport of nitrates below drip line in the CONT system, mostly because of the increased surface area subjected to precipitation/irrigation due to the absence of soil cover. Numerical modeling revealed large influence of plastic mulch cover on water and nutrient distribution in soil. The study suggests that under this management practice the nitrogen amounts applied via fertigation can be lowered and optimized to reduce possible negative influence on environment