We had these issues in the past before GMOs, and it was caused by what? Fertilizer runoff, from corn crops, causing extremely high levels of nitrogen in water.
It's not so much 'synthetic' fertilizer being the issue either - the technology behind those predate the Dead Zones by decades too. Nitrogen based fertilizers are created using the Haber-Bosch Process which was created in 1909, while phosphate based fertalizers use the Odda Process created in 1927. While synthetic fertilizers ARE used more then natural ones, switching over to natural/organic nitrogen/phosphate based fertalizers wouldn't help - We'd STILL be having high fertilizer runoff that would cause a nitrogen imbalance.
Attacking GMOs or synthetic fertilizers is a easy thing to do in this case, since it's a nice way to ignore the REAL cause of the issue here - Our ever growing demand for corn.
You get rid of GMO corn? This issue predated GMO's by 25 years. You've switched back to 'natural' corn seeds, and you're still having to grow just as much as before. You've done nothing to resolve the issue.
You get rid of synthetic fertilizers and switch to natural and organic ones? You're still going to be having fertilizer runoff that causes the nitrogen imbalance that causes these Dead Zones - The algae doesn't care if the Nitrogen is 'natural' or 'synthetic', it's going to be using it either way.
The only way this issue gets solved is if our demand for corn goes down. Less corn being grown = less fertilizers (Be they synthetic, natural, or organic) = less runoff.