It is complex but in general there are shallow 'active' water rivers/lakes which fill and empty on a month/year scale and then there are ancient deep ones that are probably not connected to the sea.
We are of course in a much much colder period than the Eocene ~50 Ma and colder again since Antarctic Reglaciation about 15 Ma so some deep lakes are water from these warm times. I will leave the optimum temperate for the Earth and its inhabitants to the individual reader.
