Although it's true that anything in the water gets into the fish through osmosis, most aquatic plant fertilizers, when properly used are safe for fish. As a matter of fact, I culture Red Russian Daphnia (among other things) as a live food source and daphnia are extremely sensitive to water quality. I use a small amount of aquatic fertilizer in daphnia bins to stimulate algae growth and it does not harm the daphnia.
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I feed the fish high quality live and commercial fish foods so there is very little fish waste. I find that if I don't supplement with a modest amount of aquatic plant fertilizer, the plants suffer and don't grow well at all.
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So all things in moderation.