Better sewage treatment plants would help a lot. When i first started keeping a boat at the Jersey shore, the back bay smelled really bad at low tide. The problem was all the small sewage treatment plants for the old shore communities were only primary treatment plants. they just filtered out the big chunks. The rest went right into the tidal bay. thru the 80s as the beach towns expanded and grew, they upgraded to secondary treatment plants, which like our trickle filters convert the waste to nitrates and phosphates. but also sanitze with chlorine. big improvement, but it fed the algae like crazy.
So the next step should be tertiary treatment plants.
http://en.wikipedia.org/wiki/Sewage_treatment
which remove or mitigate much of the waste biproduct and return nearly potable water to the bay and river systems, which all flow to the ocean.
and if combined with artificial wetland eco systems, the effluent flowing thru the wetlands will be scrubbed of all waste by the plants and bacteria by the time it hits the river, lake, bay or oceans. We just can't keep dumping it all straight to the water systems. It is just too much.
Here is an interesting thawt for all the inland reefers living in cities along rivers with muni water supplies. Every river town puts it's drinking water intake plant on the upstream side of town, and its sewage discharge plant on the downstream side of the river. But how many towns are on those rivers? Every few miles? Lucky town at the mouth of the river,,, EHH??
Have a glass of water.