Replenishment of infiltrating groundwater is known as recharge. Discharge of groundwater occurs when water emerges from the ground. In Pennsylvania, most streams gain flow from groundwater. A few streams may recharge aquifers during periods of high streamflow (such as spring run off), but receive discharge from aquifers during periods of low streamflow (such as late fall). Also, in a few areas of Pennsylvania, perennial losing streams contribute to the storage of groundwater. Specific areas where this can happen include carbonate rock valleys, deep-mined regions and where upland streams flow off highlands into glacial outwash valleys.

Unconfined aquifers are recharged primarily from precipitation percolating, or infiltrating, down from ground surface. Confined aquifers are generally recharged where the aquifer materials are exposed at the surface (outcrop).

Properly identifying the recharge area is critical in groundwater protection because the introduction of contaminants within the recharge area can cause aquifer contamination.