This study uses geographic information systems to map the hotspots level changes in underground water quality based on pH, nitrate and conductivity in Amman, Zarqa and Balqa regions, Jordan using data from 57 wells. The chemical concentration for each parameter was obtained from the Water Authority of Jordan. The data were tested according to ISO/IEC 17025 standards by the Jordan Inorganic Laboratory of the Laboratories and Quality Department of Water Authority for 2004 and 2010 and were processed using Getis-Ord Gi statistics. The study indicated that there are periodic fluctuations for the values of selected chemical elements of groundwater that are localized, creating contamination hotspots within the study regions. The pH, nitrate and conductivity all indicated specific hotspots of higher than average values in 2004 and 2010 in the Zarqa region. The evidence indicates that there are two major localized areas of high value for all parameters centered in the western Zarqa region, an area dominated by urban infrastructure and irrigated lands. These findings have implications for the management of aquifer water quality through the identification of high-value hotspots. Because the aquifers in the regions are connected, understanding the hotspots with high pH, nitrate and conductivity values may enable improvements in the water quality across the aquifer systems in the regions.