For systems that pump to the sea, the waste is pumped to large enough distance from the shore that by the time it reaches the shore again (as determined by currents and who knows what else) it is sufficiently disintegrated and decomposed to not be harmful for swimmers on the beach. Remember this from my uncle who is an engineer and works in sewage systems design, construction, and maintenance.
A distance I think he mentioned for a specific construction he was working on was 350 meters from shore, but this could be incorrect.