The Kapas Island and the Bidong Island are categorized as one of the archipelago of small islands in Malaysia. These islands are usually having hardship producing uncontaminated in groundwater supply to help the daily need of population. Groundwater samples are taken from all 13 wells from both islands and deanalyze. Groundwater at small islands are usually contaminated with contamination that is higher, resulted from salt water intrusion. Other than that, geological mapping is done as the geological structures detects contamination that is the cause of so many fractures on rocks. Furthermore, the using the hand lens. The main problem of the groundwater sources to be used for drinking and other purpose is contaminated with brine water, or in other word is salt water intrusion. Therefore, chemical elements distribution will give impact to the environment. This research is very important as a medium for groundwater monitoring in Malaysia.