This paper discussed hydrogen and oxygen isotopes and boron isotope of shallow groundwater and determined the sources of brackish water and salt water, which used the 4-hole comprehensive test well within 80 m of the aquifers of different depths in groundwater science and engineering experimental site of ministry of land and resources as the object of studying. The results show that the values of hydrogen and oxygen isotopes of salt water and brackish water in the area are generally negative, and the values of δ18O and δD do not exceed the characteristic values of marine saltwater. The δ11B‰ value is between δ11B‰ of seawater and continental freshwater and obviously lower than δ11B‰ in seawater. It proves the terrestrial origin of regional groundwater. The results show that the mix ratio of salty water in two brackish aquifers is increasing yearly by calculations, which is consistent with the increase of TDS and Cl- in the aquifer. Furthermore, it is proved that the brackish water in the study area tended to be more salty to some extent.