i am not so sure what you asking about,are you having those spot algee on the glass or green water?
if you having green water,just turn off your light for 3-4 days.
i tried before result was prefect.
if you are haing those green dot on the glass,normally what i do is use a blade or some hard card,remoev them.easy and fast.

too high nitrat might coz this due to fish waste and direct sunlight.