This study applied groundwater hydrograph and isotope analysis method to estimating groundwater balance and evaluating the recharge from sources including rainfall, river seepage and inflow through the boundary in a groundwater system. The area studied in this research is the Ping-Tung plain. The estimation results show that, from 1999 to 2008, the average annual change in storage was 0.11 hundred million tons, the average annual withdrawal was 14.08 hundred million tons, the average annual recharge was 17.57 hundred million tons and the average annual groundwater loss was 3.38 hundred million tons. Among all the recharge sources, rainfall accounts for 55.9 of groundwater recharge; river seepage, 14.3; and inflow through the boundary, 29.8.