Aims: To determine the effects of salt harvesting on ground water quality in Gongoni ward, Kilifi County. Study Design: The study design was purposive where sampling points were deliberately chosen. Place and Duration of Study: The study was carried out in Gongoni ward and its environs in Kilifi County from May 2015 to July 2015. Methodology: Sixteen sampling points were selected within the study area and sampling was done twice between May and July 2015. The water samples collected were analyzed for sodium (Na+), Chlorides (Cl-), Fluorides, (F-) Calcium (Ca2+), alkalinity, acidity (pH), E. coli, Total Dissolved Solids (TDS) and Salinity as NaCl in the Government Chemist laboratories in Mombasa. The collected data was analyzed using SPSS and Microsoft Office Excel. Results: The ground water sources in Gongoni ward registered high levels of key parameters (TDS, Salinity, Chloride, and Sodium) than the adjacent areas of Mambrui, Ngomeni and selected secondary data from Mombasa County wells where no salt harvesting occurs. Gongoni water sources had a mean TDS of 1969.00mg/L and the adjacent area shad TDS of 1050.00 mg/L. The level of E. coli and total coliform were above the Kenyan and WHO permissible limit of 0 MPN/100ml for treated water and 10 MPN/100mls for untreated water. Conclusion: Despite the elevated concentration levels of chemical parameters from Gongoni ward water sources, the differences are not statistically significant when compared to the adjacent areas of Mambrui and Ngomeni. Recommendations: The water from sources with high levels of TDS and salinity should be pre-treated to make the water more suitable for human use. Those with high coliform and E. coli bacteria should be regularly treated using the appropriate disinfection methods. It is recommended that all projects on salt harvesting should be subjected to an Environmental and Social Impact Assessment (ESIA) before implementation as provided by the Kenya Environmental Management and Coordination Act of 1999.