I recommend a dedicated fuge running at least 12 hours a day and determining if your phosphate levels are detectable to start. It is probably a good idea to test the phosphates of your fresh saltwater. I also recommend identifying the pest that you have encountered-does it blow off the sand and rocks easily with a turkey baster or power head?
I had a TERRIBLE case of cyano and it started with a little in the sand like that. After 4 months or so, all the rock, foam was, was covered. Luckily it stayed away from my corals. After various techniques to try to curb it, I realized it would take too long to go away. So I used chemiclean and that worked like a champ, I was very surprised.