Frilly, as soon as you get some bigger plants established in there they will shade the water and reduce the algae growth in there. Get planting, girl!
But you do need to move/aerate the water somehow, and it's easy to put a filter on when you install a little pump for your fountain or other aeration device. Mine just has a fiber filter that I lift out and hose off about every 2 months.
You will need to plant your water plants in pots before putting them into a rubber-lined pond because there won't be enough soil for them to root directly into the bottom of the pond. So choose a large black nursery pot - the biggest one you can get your hands on, weight it down with some rocks in the bottom, sandy soil over that and plant your lotus or water lilies. They will then be at least a foot up from the bottom of the pond so the depth is less of a problem.
My pond is only about 2ft. deep, and I set the pots for my water lilies on top of cinder blocks in the water so the tops of the pots are then only about 6in. below the water surface. The fish like to hide in the tunnels of the cinder blocks, too. (place them in there sideways so there are tunnels) Using cinder blocks you can place a pot in your pond at just about any height you want.
