You should first sanitize your freshwater hose thoroughly; it may be filled with algae too. Mix about 1 ounce bleach in a gallon of water. Hold both ends of the hose up in the air, pour the bleach in one end, and screw them together. Slosh it around and let it set for about 12 hours. Then dump it out.
Make up a fresh batch of bleach in the correct amount for your system (1/4 cup bleach for every 15 gallons of tank capacity, plus the water heater volume). Put the bleach in about a quart or more of water. Put the hose on the fill, pour the bleach in, and then connect the hose to a spigot. Fill the fresh tank.
Open all the faucets, hot and cold and run through until you smell the bleach from each one. Be sure to run enough hot to fill the water heater. Dont' forget the outside shower if you have one. Then let it stand 12 hours or longer.
Drain the fresh tank and fill it with clean water. Run through the entire system until no more bleach smell. This may take a couple of drain/refill cycles on the tank.
At this point you may have to clean the filter again.
If you routinely fill with non-chlorinated water, you may have to sanitize often.