I almost always shoot aperture priority. Shutter speed is irrelevant most times, as long as you're hitting above 1/60, you should be able to freeze the fish and not get motion blur.
Honestly though, my aperture is usually wide open to allow more light in because I never bother with a flash. I haven't used my flash in years. Perhaps I should break it out. I think I do ok with ambient lighting though:
I'd highly recommend getting fixed lens with a wide aperture, like a 50mm f/1.8 or something. The 50mm canon lens is around $90 new, not sure what the nikon variety would be.
I also only shoot in raw and convert and do all editing in Adobe Lightroom. Let me know if you'd like a copy. I can send one over to ya. It's a great program.