Because Zaton is located on a narrow bay, the water almost stands still.
Now the government is working on a better drainage, but before some time and also now the dirty water of the households in Zaton dump their water in the bay. Because of the water is standing still, the sea can't wash everything clear.
But no worries, you can't see it, it doesn't smell bad and it's not unhealthy. The dirty water is not dumped on the coastline, but deeper in the bay.
Government authorities frequently check the waterquality.
It's still of moderate quality, but it's less than the other areas around Dubrovnik.
So don't think it's a real threat or danger.