While a few tropical peatlands remain in pristine condition, many of them, especially in Southeast Asia, have been degraded and have been subjected to drainage, deforestation or fires. At the largest peat deposit in Brunei Darussalam, the Badas peat dome, anthropogenic disturbances arising from urbanisation and land use changes in the past decades have resulted in deforestation, peat subsidence and groundwater drainage. We investigated these disturbances along two transects established at the Badas peat dome via a combination of approaches: (1) topographic survey, (2) seismic refraction survey, (3) rain gauge monitoring and (4) groundwater monitoring via piezometers and slug testing. In addition, groundwater samples were taken from piezometers for water chemistry analysis. This research demonstrated how excavations have led to the creation of lagoons, resulting in changes to the structure of the peat dome, leading to groundwater drainage. The drainage has caused 15 cm to 45 cm of peat thickness to dry out. In addition, with the removal of the peat layer and the establishment of artificial lagoons, surface water can now directly infiltrate into the sand layer, causing the second transect to have a lower groundwater level. Finally, groundwater drainage, evapotranspiration from the lagoons, and possibly tidal influence as the peatland is draining towards the South China Sea less than 3 km away, caused changes to the groundwater chemistry, causing increased salinity and Dissolved Organic Carbon (DOC), showing that peat degradation has been occurring in both transects.