Aquifer mergence zones are erosional unconformities that hydraulically join interlaying aquifers. In the East Newport Mesa in Orange County, Southern California, aquifer mergence zones may provide a pathway for potentially impaired low-quality groundwater of the shallow, semi-perched aquifer to migrate into the underlying regional, potable, confined aquifers. Major ion and stable isotope results imply that vertical mixing is occurring locally between the discrete shallow and deep groundwater endmembers. Vertical mixing is suggested by anomalously young radiocarbon age-dates of deep groundwater units. Radon-222 results show that shallow groundwater is discharging from the mesa, and is also actively intruded by surface water. Mixing of shallow and deep waters at these mergence zones may pose a threat to the deeper regional aquifer system.