The dry season impacts clean water availability in Indonesia, particularly on small islands; however, there are few comprehensive studies of water availability on small islands. The aim of this study was to assess clean water sources and the obstacles to accessing clean water on small islands. We used a combination of structured questionnaires and interviews along with direct observations on two small islands in Indonesia, Belakang Padang Island and Labu Island. On Belakang Padang Island, we interviewed the water resource manager in October 2022 and May 2023, and surveyed 61 households in Tanjung Sari subdistrict RT No. 002/RW No. 002 in October 2022. On Labu Island, we interviewed the staff of the seawater reverse osmosis (SWRO) system and surveyed 35 coastal households in September 2023. On both islands, the government has improved residents’ access to clean water by constructing SWRO facilities. The small SWRO facility on Labu Island ran more efficiently and stably as it was powered by a generator. The larger SWRO facility on Belakang Padang Island experienced disruptions during periods of unstable electricity generation supplied by the State Electricity Company. The absence of septic tanks pollutes the surrounding area and increases the risk of contaminating underground water and pipe networks (reservoirs and SWRO) during high tides, and seawater used for SWRO’s raw water. Our findings recommended the use of generators or sustainable generators for SWRO on small islands to achieve stable SWRO operation, as well as the use of an appropriate septic tank for coastal communities on small islands.