After talking to people at Drummers on Sunday I started to do the spring clean up on the pond. I started by checking out the pump to make sure things are functioning. I plugged it in and it seem to be working even though it was a bit noisy. I removed the hose that was going to the upper waterfall pool and pointed it to the yard. Before hooking up the pump I removed as much algae as I could with a net and put it in my compost bin. As soon as I didn't think I could get more I put in the pump and started draining the pond.
As the pond drained I started cleaning the liner and the rocks that lined the pond. I used a toilet brush as it was the only thing around the house I wanted to risk putting algae on. It was clean and relatively new. I also tried to net out more algae, which cause the pump to suck in algae as well. So a number of times I took the pump out to clean the algae from it and then put it back in. When the water level got to a point where the pump could not pump any water out I started to bail water out and also used the garden hose and my brush to clean any algae I could see from the liner and the rocks. Eventually the pond was pretty dry and what water remained was clear.
After every thing was cleaned up to a point that I felt it was good enough. I put the hose back where it was pointing in the upper pool and started to fill the pond from the upper pool (as it was closer to where the business end of the garden hose is usually kept). As it filled I watched for debris and algae that I missed pop out and I removed it as a I saw it. Once the pond was filled I added 110ml of PondCare Ecofix Bacterial Pond Clarifier to the water to start the bacteria colony. I also added a insect tablet to the upper and lower pools to help keep the mosquitos down. I hope add more Clarifier in about 3-4 days as directed by Drummers and the bottle.
Below are a couple pictures of the pond as it fills. As you can see the lower pool has a couple deeper areas but not too deep.