There really isn't much to say about the waterway; just a few things.
At 10HP per hit, it's just not smart to hit the spikes. You may need that health for the upcoming battle. With practice, all of them can be avoided with normal jumps.
Curly needs draining after the incident with the core. Near the end of the artery, you'll come to an area where the currents are pulling you hard in all directions, but eventually, you'll get to a small exit near the top. This is where you need really good timing. There will be a slight overhang, jump when you are on top of it, and get to the oddly-placed cabin. You can save and restore health there, and if you have Curly with you, not going there will cause Curly to shut down permanently. If Curly is with you, look at the bookshelf, then take a rest. Curly will stay on the bed after you rest, so attempt to talk to her after checking the shelf to drain the water from her. Once that's done, save, then go back over to her and when prompted, say no, you don't want to leave her behind. You won't be able to come back here after you beat Ironhead, so you don't want to leave her here.
Ironhead can be difficult without a proper strategy. Getting behind him and rapid firing at his back with super missiles can be an effective strategy. Other players prefer to use the blade.