Onsite wastewater treatment systems (OWTS), commonly known as septic systems, are increasingly recognized as a potential source of nitrogen in the shallow groundwater. Our objective was to investigate the effect of hydrological and biogeochemical factors in the vadose zone on the fate of effluent-borne N in the drainfields of a drip-dispersal OWTS. Three lysimeters (152.4 cm long, 91.4 cm wide, and 91.4 cm high) were constructed using pressure-treated wood to mimic OWTS drainfields. Each lysimeter had three distinct layers of gravel–sand mixture, soil, and commercial sand. A drip tube, which was covered with commercial sand before planting St. Augustine grass (Stenotaphrum Trin.) on the top and sides of the lysimeters, dispersed 9 L of septic tank effluent (STE) per day on top of the stacked layers. Each lysimeter was instrumented with 10 multi-probe sensors to determine the water content, electrical conductivity (EC), and temperature in the center and sides of sand and soil layers. Leachate samples were collected over 67 events, which consisted of one sample every 24 h for 15 d (n = 15) and weekly flow-weighted composite samples (n = 52). In all events, the pH, EC, and chloride were lower in the leachate than STE. Daily multi-probe data showed that EC was greater in the center than sides of the lysimeters due to more STE interaction. Sensor water content data were used to calculate water filled porosity (WFP), which was greater in the soil (0.55–0.9) than sand (0.07–0.32) due to the textural differences. Mean total N was 70 mg L−1 in the STE, which reduced to 27.4 mg L−1 in the leachate likely due to the denitrification in the soil layer. The dominance of NOx–N in the leachate (61%) as compared to STE (0.6%) was attributed to the nitrification in the sand layer. Higher proportion of organic N in the leachate (39%) than STE (16%) suggests that organic N was mobile in the vadose zone and leached below the drainfields. We conclude that hydrological and biogeochemical controls in the vadose zone play an important role in N transformations and transport of NOx–N and organic N below OWTS drainfields.