[This dataset is embargoed until August 31, 2026]. This dataset includes measurements of groundwater levels, salinity, and pH collected from 36 dug wells, along with rainfall data, on the Indian Ocean island of Karainagar, Sri Lanka, spanning the period from 2019 to 2024. Karainagar, the study area, is one of seven islands located off the coast of Jaffna in northern Sri Lanka. This rectangular island is bounded on three sides by the Palk Strait, while the fourth side faces the Jaffna Lagoon and is connected to the mainland by a causeway. Karainagar covers an area of approximately 22 km², including inland water bodies. Thirty-six dug wells—used for agricultural, domestic, Kovil (Temple), and public purposes—were inventoried. These wells were monitored to track groundwater levels and key physicochemical parameters, specifically salinity (measured as electrical conductivity, EC) and pH, on Karainagar Island. Full details about this dataset can be found at https://doi.org/10.5285/ba22d53b-4eee-48a1-b6f3-653d252c0358