Urban karst aquifers are threatened by anthropogenic activities, especially in semiarid developing countries. Recent water-sampling campaigns assessed the extent of groundwater-quality impairment in the Wadi Shueib in Jordan by a comprehensive hydrogeological and hydrochemical characterization of groundwater, wastewater, and imported water with its endmembers Lake Tiberias, Yarmouk River and Mukheiba wellfield. The results of a ternary mixing model with the mass ratios of Cl−/Br− and Ca2+/Mg2+ indicate that Lake Tiberias and Yarmouk River provide most of the imported water at the time of sampling in 2017 and Mukheiba wellfield provided minor amounts. The similarity in seasonal variations of Br− concentrations in the springs and the imported water revealed that imported water has generally a greater impact on groundwater than wastewater. However, the Br− concentrations also showed that the spatial wastewater impact is more visible towards urbanized areas due to increased infiltration of pollutants. The analysis of historical data series demonstrated the long-term urban impact on groundwater by an electrical conductivity increase over several decades, particularly since the mid-1990s, which is related to a doubling of Jordan’s population since that time and the associated urban growth. In this context, increased chloride and sulfate concentrations are noticeable due to the increased impact of more highly mineralized imported water and wastewater and decreasing recharge of low-mineralized rainwater. This study showed the hydrochemical differences in the Wadi Shueib groundwater system and serves as an example for the spatial and long-term response of karst aquifers to anthropogenic, seasonally variable input of imported water and wastewater.