Brunei has made significant progress in agricultural development over the past four decades. However, crop production, such as rice, is still insufficient to meet the demands of the growing population, mainly due to the scarcity of water resources, acidic soils, and advancing environmental deterioration. This study conducted soil and groundwater investigations at three selected rice cultivation sites in Brunei Darussalam. The geoelectrical resistivity method using the vertical electrical sounding (VES) technique delineated subsurface stratigraphy with resistivities ranging from 1 to 180 Ωm in the investigated area. A potential aquifer zone was inferred in one of the surveyed areas with resistivities ranging from 10 to 150 Ωm at depths of about 40 to 60 m below ground level. Groundwater levels were also shallower in irrigated sites compared to non-irrigated sites. Groundwater physicochemical properties revealed high alkalinity and mineralisation, as evident from high magnesium, bicarbonate, ammoniacal nitrogen, and iron, as well as pH values in the water samples, believed to be the effects of leaching of salt ions into the shallow aquifer through infiltration recharge. In addition, soil physicochemical properties showed that the soils near a pumping well were more acidic, had lower moisture, and total nutrients, likely due to the effects of groundwater pumping. Our results demonstrate that future irrigation activities need to consider local aquifer characteristics, groundwater flow paths, and nutrient transport to ensure sustainable development in agricultural areas.