The sea level changed in the geological past for example Quaternary sea level change. Do the chemical composition of groundwater change in glacial and interglacial period?
If mixing happened it would affect the quality for sure, but fresh water always rest over saline water due to difference in density and mixing need time. When fresh water and saltwater meet in an estuary for example, they do not always mix very fast. The problem with sea level change is mostly the sea water intrusion which can go for several kilometers affecting groundwater aquifers. Sea water intrusion can also increase if there are decrease in the fresh water discharge from rivers to the sea.
Yes. In Florida, USA, due to destruction of wetlands there have been issues with sea water contaminating potable water as well as septic tank water getting into water tables. They are now working on reversing the trend by trying to restore wetlands to some extent as well as providing connectivity among bodies of fresh water.