It sounds like you have poor water and lots of iron in it. Right now, I would not deal with the iron issue until the water clears up. First, do not shut the filter off. Let it run and use regular bleach to get your chlorine up. If it is new water, I am not sure you need anything for algae.

Try to get your chlorine up and just let it run. The chlorine and filter will do its job, with time.

When the water clears up, I am guessing that the liner will be brown and you will have to hit it with and acid to clean it up..