Pulau Kapas is tropical island which dominantly depends on land-supplied and groundwater for freshwater sources. The groundwater quality was monitored monthly, to identify the possible factors effecting the groundwater quality throughout May to October 2022. Physico-chemical parameters were in-situ measured and groundwater were collected for nutrients analysis in the laboratory. The concentration of ammonium, phosphate, nitrite, and nitrate were in the range of 0.07-1.08 mg/L, 0.00-0.06 mg/L, BDL-18 × 10-4 mg/L and 0.01-0.19 mg/L, respectively. The cluster and principal component analysis unveiled the seawater intrusion for freshwater needs was the dominant factor affecting the groundwater. Followed by the dissolution of soil particles surrounds the groundwater table, and the surface run-off by rainfall. In conclusion, the groundwater was affected by geogenic factors as it was not extensively extracted due to movement control order of Covid-19 event. This has provided significant insight for a better management plan in sustaining the groundwater of Pulau Kapas.