Isolated islands are vulnerable to shortages in water availability, necessitating the use of hybrid water sources. There is a knowledge gap of unknown microbial diversity in the hybrid sources. The present study collected water samples from different water sources and water treatment processes on an isolated island in the South China Sea to explore microbial diversity in a full-element hybrid water supply system and analyze the effects of environmental factors. The primary conclusions were as follows: (a) Currently, chemical indices generally pass the WHO standards, except for high pH levels. (b) The driving factors for microbial diversity followed the order of type of source water > temperature > UV254 > turbidity > materials of containers > oxidation-reduction potential > pH > OD600 > ion concentration. Microbial dissimilarity was primarily affected by temperature and organic matter, while distribution distance had a slight effect on the dissimilarity in the small-scale ecosystem. (c) Biological and chemical safety standards restrict the application of atmospheric water using metal-organic frameworks while the balance of water influences the exploitation of freshwater lenses on the isolated island.