How long were you growing out the brine cultures? Nauplii are very small but adult brine shrimp can get pretty darn large (3/4"). As long as you soak them in something like Selco/Selcon and get them gut loaded, it gets enough HUFA's to the fish to be healthy. Just don't enrich your main culture, you need to strain off part of the culture. Otherwise, you risk contaminating your culture.
Brine shrimp are MUCH easier to culture then phyto. I ended up going store purchased phyto, as in the end it's a lot easier. It's harder to crash a brine shrimp culture although it is possible to crash brine shrimp as well. They are just more forgiving. If you treat a brine shrimp culture as you would your normal tank, it will be a good self-perpetuating system.
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