Jaffna is a land of wells, where water rises through the limestone. This phenomenon of innumerable wells with fresh water in the Jaffna Peninsula and in the surrounding islands resting on sand has attracted the attention of early navigators like the sixth century author of Cosmos Indicopleustes. This phenomenon found also elsewhere in islands of coral reefs, where the wells with abundance of fresh water is dependent on the tide, has been-attributed to the fact that the rocks underneath are "magnesian limestone and coral, overlying a bed of sand". Tennent was convinced that the extent to which fresh water is found in Jaffna "is directly connected with percolation from the sea." In Jaffna, the wells gggg~ are below the sea level. The rainwater in November fills the well sometimes to the brim but the water sinks to the uniform level during the dry season and remains the same till the next rain. Wells below the sea level never become dry of themselves even during the time of drought. According to an observer, "the contents do not vary with the tides, the rise of which is so trifling that the distance from the ocean, and the slowness of filtration render its fluctuations imperceptible".

There are three wells, which deserve special mention. The well at Puttur, where the soil is said to be light and the surface of the ground hollow, is more than 140 feet deep and the water is fresh at the surface, brackish in the middle and quite salty below. It is said to be directly connected with the sea " by means of a fissure or a channel beneath an arch of magnesium limestone,[and] rises and falls a few inches in the course of every twelve hours".

Water level on another well at Navakiri rises and falls a little like the Puttur well.

Another well at Tellippalai, which has a cavern containing water, remains unaffected by rains or drought, maintaining its depth at all times.

There are more than 600 kulams or ponds in the Peninsula. These are not man-made but are natural depressions, which arise due to the solution of the limestone by the action of the rainwater and by the crumbling of the top portion of subterranean limestone cavities. They also serve to conduct the excess rain water underground

The underground water storage supports not only a very high population as drinking water but also serve as good water for watering garden crops.