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Algae is a product of excess nutrients. Excess nutrients are usually on the substrate. I'm not sure how well a protein skimmer would increase the water quality.
protien skimmers actualy do work in fw. just very very very ineficiantly. and i mean very ineficently. i cant stress enough how ineficient they are. with out salt the water has less of an ionic charge so the bubles have a hard time attaching themselfs to waist. its so ineficient that its just a wait of energy.
I run a attachment skimmer off my fluval 304 at night. It keeps my co2 down and it make the surface sparkel. I would think that the excess stuff foating around would help a higher nitrate level but, not enough to matter. It just for looks
it will work in fresh water. get this straight. it will work. just very very very very eneficiently. ive tried it out. it works. it just wont produce a cup of skimmate for a cupple of months. if you really want to do it, get a serface injection like the cpr remora. but its not going to work very well