This study compares water quality parameters, shrimp growth and mortality rates, and biomass at harvest in two ponds of equal size, seeded with the same density (7 m2) of White Spot Syndrome Virus (WSSV) and Monodon Baculo Virus (MBV) negative post-larvae (PL)-20 of shrimp, Penaeus monodon in the Vellar estuary of South India. The primary difference between the ponds was the water source; one was filled from the estuary and the second with water from bore wells with high alkalinity. Temperature in both ponds was similar and reached 320C after 185 days of culture. Dissolved oxygen (DO) levels were within the acceptable range although levels in the alkaline pond were near the lower limit for the last 90 days before harvest. Salinity levels were similar in both ponds, above optimal levels, and increased over the 185 days. Alkalinity in the estuarine water was typically <50 ppm and again 200-320 ppm in the alkaline pond. In the alkaline pond, beginning on the 75th day mineral deposits was observed covering all parts of the shrimp including the eye and the inner gill chambers, and by harvest, 42% of the shrimp showed this coating. Elemental analysis identified the major constituents as calcium, phosphorus and manganese. Survival rates in the estuarine-water-fed pond was 92% with a total pond biomass at harvest of 1.65 tons ha-1 compared to survival of 79% in the alkaline pond and a biomass at harvest of 1.020 tons ha-1. When well water must be used, its alkalinity should be monitored and diluted with water from other sources.