Why does the ocean seem much cleaner than the bay I live near
I had the same experience when I lived in Cardiff, South Wales. When I lived there, the waters around Cardiff were always greyish and uninviting, but the further away one got, the more blue-green and transparent the sea became. Fifty miles west on the Gower coast, the water was pristine and beautifully transparent, more like the Mediterranean.

The reason for this was two fold: a lot of effluent from the city, including sewage, was discharged into the sea, and the river Taff, which runs through Cardiff, brought down a lot of industrial effluent from the Welsh valleys. It is a matter of common sense that the sea dispersed and diluted the pollution the further away from the big city one looked. I understand that the river and the city are much cleaner now, but I think the murky waters of Melbourne which you describe are due to the same sort of causes which many years ago fouled the waters around Cardiff.