Rapid population growth and increasing demand for the modern settlement has led to the increase of environmental pollution. Limestone quarry is one among the activities that affect environment and ecosystem in Pemba Island-Zanzibar. Quarrying activities brought an inevitable destruction to the environments ranging from excavation, soil and land degradation, loose of biodiversity and water pollution. This study reports the impact of limestone quarries on groundwater quality based on analyses of various physico-chemical parameters of groundwater. Ground water samples were collected during the wet and dry season of 2016 from nine different wells in vicinity of limestone quarries. One groundwater sample, which was located about 5 kilometers from limestone quarries, was collected as a control. The result shows that the groundwater have an elevated level of pH, total dissolved solid, Electrical Conductivity, total alkalinity, as compared to control sample. Also the concentration level of Ca2+, Mg2+ and Na+ slightly increases in all samples from dry season to wet season. This is probably due to the mixing of surface pollution and dissolution of limestone rocks. The study revealed that the nitrate and potassium concentrations are very high in the well nearest the limestone quarries. It is likely due to percolation of fertilizer from agricultural runoff stagnated nearby limestone quarries. This study shows that a conceptual physico-chemical interpretation of the results from water samples provides information of groundwater contamination, which is mainly derived from agricultural runoff and stagnated nearby limestone quarries. This study recommends that the quarrying activities should be minimal towards the subsurface level in order to reduce the possibility of aquifer contamination.