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So very sorry you lost your pet. I've read/heard that fluctuations in water temp can be particularly deadly. Was this baby captive bred? Could have been a parasite or infection if not. Cohabitation between species is generally frowned upon and can cause death from stress or communicable disease. If you are going to keep another you might consider a 20 gallon for a hatchling, use a water heater with a reliable thermostat and reduce stress as much as possible. I am no expert on crocodilians but I have been doing a TON of research on them as we're planning on getting a couple very soon!
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