i don't think anyone knows, but I'd bet its a manmade change.

Look at the canal, most of it has houses every 100' with septic systems, many of which leak. Not to mention suburban runoff. Phosphorous inputs etct. In lots of places, these sort of nutrient rich inputs cause algae blooms. Look at most of the lowland lakes in the US.

You don't see these problems in the sound because it flushes out so rapidly due to tidal flow. However it takes a much longer time for the canal to flush out. Compound nutrient increased inputs with a decreased capacity to filter out the plankton (heavily harvested or overharvested clams and oysters) and you have a recipe for algea blooms and low oxgen levels.

Just my $0.02