Carbon credits would be perfect. In fact, if oceanographic organizations such as ORCA could get themselves into the benefactor stream (I'm not sure what the right term is), that would be great. Intuitively, it's not a stretch, either - massive swaths of hypoxic water could have huge impacts on global warming (lack of oxygen-producing organisms also means lack of carbon-consuming organisms, since they're one and the same). But unfortunately our political system is too complex and unless you've already got the funding to pay lobbyists you're just not going to get very far.
A number of people in the Chesapeake basin point the finger at chicken and pig farms in the region due to their controversial use of manure lagoons [1]. To the best of my knowledge these industries aren't heavily subsidized like corn and soy.
Then there's the whole issue of baselining. What's normal for the Mississippi river outflow? We've been observing the impacts to the fisheries there and the Chesapeake for hundreds of years, but we've only been measuring DO for a few decades and DO is far from the only thing that impacts fisheries. Further, the Mississippi dumps a ton of relatively still water that's full of tannins directly into the relatively still and warm gulf. I'm nowhere near qualified to say this conclusively, but I'd bet there have been yearly cycles of hypoxia there for millennia. Does this multiply or dampen our impacts?
This is a crazy complex multi-headed monster that looks completely different in every region it inhabits. For every one of these massive hypoxic regions there's a ton of other smaller ones. Next time you're bored take a look at the waterways in your area on Google maps, especially where small local canals or drainage ditches empty into larger bodies of water. Then go look at the topography of the area and try to back-of-the-envelope account for what all is pouring out of there. Then go do that for a completely different region. The diversity if nutrient inputs is insane.
The only reliable long-term way I can see to fix the problem is to get people to understand the impacts of their actions, and to associate those impacts with the things that they buy, consume, and produce. When you flush the toilet your poop goes somewhere. The same is true with your lawn clippings, farm waste, fertilizers, antibiotics, birth control, etc.
1: http://nc.water.usgs.gov/flood/floods99/photos/IMG003.html
I ask this non-rhetorically: how the hell does anyone turn that on its head, especially without government involvement?
The Ocean Research and Conservation Association is a nonprofit that's trying to promote the visibility of this problem (hypoxia caused by harmful blooms). They're doing this through the use of very low cost in situ sensor networks [1] and broad spectrum toxicology assays [2]. It's headed by Dr. Edie Widder [3], the scientist who got the first footage of the giant squid on last year's Discovery Channel cruise.
In combination with measuring physical/chemical parameters, they can automatically measure biological parameters of the environment. They've done this by miniaturizing and cost-reducing bathyphotometer [4] technology.
To the best of my very limited knowledge nobody else is looking at the problem this way. Everybody else measures physical/chemical parameters, and either infer what's happening to the biology, or they do point or small area biological sampling on an infrequent basis. And because it's so damn expensive there's always a big tradeoff between temporal and spatial resolution. With techniques like that everything is aggregate and there's little ability to tie specific action to specific consequences, let alone enforce any kind of feedback loop.
One of ORCA's biggest goals is to create a realtime water health gradient map that's promoted to and accessible by the general public. In a perfect world this would be used on the news right alongside the weather report.
I hate to cast a light of negativity but frankly I doubt they'll ever pull this off. Not because of lack of technical ability or people with the passion to do the work, but because of lack of stable funding. What's crazy is their technology is downright cheap, especially compared to the magnitude of the problem. If they could ever pull together the funding to engineer for manufacturability and do a full volume run, it'd be orders of magnitude less expensive.
I freely admit that I suck at marketing, so the best I can offer is a shameless plea. If this problem is important to you do something to solve it. Read up on nutrient limiting and how it impacts hypoxia. Find a polite way to tell your neighbor that their super green lawn might be sucking the life out of the waterways. Spend a bit more to buy your meat and produce from farms that limit runoff. If you have loose change, donate to organizations like ORCA or perhaps to someone more local to you.
1: http://www.teamorca.org/cfiles/kilroy_technical.cfm 2: http://www.teamorca.org/cfiles/fast.cfm 3: http://www.ted.com/speakers/edith_widder.html 4: http://www.teamorca.org/cfiles/biolum_study.cfm
Disclosure: I'm a former ORCA employee, but otherwise I'm no longer affiliated.
Edit:
Bathyphotometer link [4] refers to a larger, more expensive model Edie designed for the US Navy. See edited [1] for reference to smaller cost-reduced version.