Well, If Ganodorf Is able to take over all of hyrule and nearly destroy it when he has the triforce, he was almost as strong without it. Without it, he destroyed the Deku Tree, filled a cavern with Dodongo's and Filled a fish with Ceatures. Maybe Ganondorf was theone why Jabu-Jabu is large. When he took over Hyrule and almost destroyed it, who knows what happened to life and water etc.?