I have lots of black spot that looks like fungi spots but probably alge, how do I clean those spots?
Already filled in my water in the pool and the problem area is 9ft. Deep please help

Do you need a good clean out and more chlorine added ? I guess so because you can't swim in anything like that !

Could be you will like this answer better, although more work for you. The algae in the bottom of your pool, if not cleaned out, will probably cause eye infections to swimmers.

This is what I am talking about::

The first thing you need to do is get the water balance tested. This can be done at either a local pool supplies store or by yourself if you have a test kit. More often than not, the cause of algae is your water balance being off and your chlorine/bromine is no longer effective. There are three main parts to water balance: Total Alkalinity, pH, and Chlorine/Bromine level. They must be corrected in that order. Provided your Alkalinity and pH are within a normal range (Total Alkalinity 80-120, pH 7.2-7.6), you should treat the algae with a chlorine shock. I strongly suggest using the strongest shock available in powder form (you probably don't want to use liquid Chlorine). If the pool has a vinyl liner, you need to brush the bottom and all sides with a nylon brush. If it is a cement pool, you can use a wire brush. After brushing all sides and the bottom of the pool, mix the powder shock in a bucket of the pool water. One pound of shock will treat 10,000 gallons of water. However, because you need to super chlorinate, you will need to put in at least one extra pound of shock. For instance, if you had a 30,000 gallon pool, you would super chlorinate with 4 pounds of shock. Keep people out of the pool for 24 hours if possible. After the shock is applied to the pool you will notice the water may turn a milky white color, or may have white particles. That white color is dead algae, and you simply must run your filter all day every day until it clears. If you want to you can use a water clarifier, which will bunch up some of the smaller particles your filter is not catching, and may speed the process. It is very important you keep an eye on your filter pressure while you kill the algae. When it gets too high, you will need to backwash, possibly as many as 2-3 times before the pool is clear. That should take care of the problem. The most important part of the process is getting your water tested at a pool supplies store. If you have a Leslies Pool Supplies in the area, I strongly suggest their service. With a little patience and money, the problem should be gone within a couple days

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you will find a complete picture of how to treat Fordyce spots.

What has spots on a penis have to do with pool cleaning ?

The information these guys have given you on superchlorinating is wrong, for instance a 30,000 gallon pool to shock it you need 1 lb per 10,000 gallons, to kill algae you need 3lbs per 10,000 gallons. Black algae is very tough to get rid of it. You can try something called black treat or draining your pool and acid washing it.