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I usually got Hydra from overfeeding newly hatched baby brine shrimp. My friend Delores Schehr of Wet Thumbs Aquatic put me on to "fluke tabs". Use 1/2 tablet for each 10 gallon of water. Crush it and mix it in a small container of tank water and just dump it in. Not harmful to anything in your tank and the Hydra will be completely gone in less than two hours.
Just curious.. what brand of brine cysts are you using? I have used some brands that are really bad about having too many hydra ephippia, and other brands that have had no problems at all.