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Once you jump into the water, the battle has "officially" begun. Nothing really happens right away, but Hydrus the Electric Eel swims around looking around, presumably for you. The instinct is to swim closer to him, but actually you'll want to keep a respectable distance; he won't notice you if you're too close. When he finally spots you, he'll make a noise and start to surface. Once again, try to keep your distance because the three spikes on his back will electrify you if you're too close when he surfaces. Swim instead in the opposite direction he is while staying directly over his back. If you've done this right (and it may take a few passes to get good at it), Hydrus' tail will come up right under you, giving you a chance to latch onto him.

Once you've grabbed ahold, Hydrus will skim the surface for a while, letting parts of his body sink and rise as he snakes around the lake. When the area you are on surfaces, run as far as you can along his back before he submerges again. It is important that you grab back onto his back before going underwater because if you fall off the whole process must be done over.

The three spikes on Hydrus' back are your first concern. Each time they hit the water, an electrified field will appear, and if you happen to be in or touching it, it will take a large chunk of your life bar. When it's out of the water though, you need to quickly run up to it and stab the glowing spot at its base. This will permanently disable the electric field for that spike. Repeat for the two remaining spikes.

The ONLY magic weakpoint is on his head, and unless he decides to submerge completely (which he does on occasion) you should have no problem charging a couple stabs and finishing off the beast.

Note
This boss is no different on Normal or Hard Modes