The HYDRUS-2D model was experimentally verified for water and salinity distribution during the profile establishment stage (33 days) of almond under pulsed and continuous drip irrigation. The model simulated values of water content obtained at different lateral distances (0, 20, 40, 60, 100 cm) from a dripper at 10, 20, 30, 40, 50, 60, 70, 80, 90, 100, 120, 140 and 160 cm soil depths at different times (5, 12, 19, 26 and 33 days of profile establishment) were compared with neutron probe measured values under both irrigation scenarios. The model closely predicted water content distribution at all distances, times and soil depths as RMSE values ranged between 0.017 and 0.049. The measured mean soil water salinity (ECsw) at 25 cm from the dripper at 30, 60, 90 and 150 cm soil depth also matched well with the predicted values. A correlation of 0.97 in pulsed and 0.98 in continuous drip systems with measured values indicated the model closely predicted total salts in the root zone. Thus, HYDRUS-2D successfully simulated the change in soil water content and soil water salinity in both the wetting pattern and in the flow domain. The initial mean ECsw below the dripper in pulsed (5.25 dSm−1) and continuous (6.07 dSm−1) irrigations decreased to 1.31 and 1.36 dSm−1, respectively, showing a respective 75.1 and 77.6% decrease in the initial salinity. The power function [y = ax−b] best described the mathematical relationship between salt removal from the soil profile as a function of irrigation time under both irrigation scenarios. Contrary to other studies, higher leaching fraction (6.4–43.1%) was recorded in pulsed than continuous (1.1–35.1%) irrigation with the same amount of applied water which was brought about by the variation in initial soil water content and time of irrigation application. It was pertinent to note that a small (0.012) increase in mean antecedent water content (θi) brought about 8.25–9.06% increase in the leaching fraction during the profile establishment irrespective of the emitter geometry, discharge rate, and irrigation scenario. Under similar θi, water applied at a higher discharge rate (3.876 Lh−1) has resulted in slightly higher leaching fraction than at a low discharge rate (1.91 Lh−1) under pulsing only owing to the variation in time of irrigation application. The influence of pulsing on soil water content, salinity distribution, and drainage flux vanished completely when irrigation was applied daily on the basis of crop evapotranspiration (ETc) with a suitable leaching fraction. Therefore, antecedent soil water content and scheduling or duration of water application play a significant role in the design of drip irrigation systems for light textured soils. These factors are the major driving force to move water and solutes within the soil profile and may influence the off-site impacts such as drainage flux and pollution of the groundwater.