In Dili, the capital city of Timor-Leste, water pollution is rapidly getting worse. This study aims to reveal a pollutant discharge mechanism and to propose a feasible water quality preservation measure even at the citizen level. Water quality survey and water level survey at 13 wells and 16 streams in four watersheds were conducted. As a result, there were two types of basins. One of which had small groundwater depth throughout the watershed, and another one had larger groundwater depth in the middle- and up-stream. The former had a large outflow which equivalent to that of Japan's excreta or miscellaneous wastewater. The latter had small runoff depth and one order smaller discharged pollutant. In the former case, leaky septic tanks may be filled much faster than expected. In the watershed with small groundwater depth, it is necessary to restrict the use of water in the waterway and to switch the treatment method from which relies on infiltration to a watertight septic tank with regular maintenance.