Here's a piece I wrote about "The Blue-Green Plague" back in July of 2013:
https://donmeredith.wordpress.com/20...-green-plague/
Agricultural and residential runoff are definitely contributing factors, as is the general warming of our lakes as a result of ongoing climate change. Cyanobacteria are in most of our lakes and ponds and provide food for many species of animals and contribute to the food chain. The problem comes when an excess of nutrients, such as phosphorus and nitrogen, enters the lake and allow the cyanobacteria to increase rapidly, robbing oxygen from the water and introducing lethal toxins. It's a complicated process and it's going to get a lot worse.
Pumping water into lakes, etc. and flushing the lakes would help, but they are expensive processes and don't really solve the problem: our over development around lakes and streams, and climate change--yes it's real and it's here.