To summarize and add to the previous comments:

Bioware:
Toxin Extractor and Pathogenic Defense; sea water isn't always the cleanest...
Chemical Gland that produces 'ink' like and octopus.
Clean Metabolism - to 'hide' your scent better from predators.
Synthacardium 2

Cyberware:
Internal Air Tank with helium (to flush residual nitrogen out of the lungs - see M&M pg.31. Not sure if that'll work with natural gills, though)
Cyberfins - almost a necessity.
Biomonitor linked to Eye Display - to help avert problems.
Cybereyes w/Ultrasound, Lowlight, Flare Compensation.
Chemical Analyzer - to alert you to any nasty substances in the water.
Cyberears w/Damper, Select Sound Filter, and Spatial Recognizer(if GM allows it to function under water - see pg.111 CC) could be useful.
Induction Datajacks only - to avoid problems with water and/or pressure.

Genetech:
Glucagon synthesis
Erythropoietin synthesis (or P4MO treatment if your GM declines Genetech)
Cold microadaption

Gear:
Gyrojet Pistol
Colt Water Carbine
Speargun
Olfactory Camouflage (T:AL pg.131)
Diving Armor(!)
Compensator and Belt, Wet suit, Dry suit, and Fins

If you are planning on dicing to 200 meters, or more, cut down on cyberware (at least if your GM chooses to use the Stress rules in T:AL) and/or encourage your GM to use the optional rule of making internal headware slip past stress tests (as per T: AL p.130).
A transducer and some form of radio might also be good, for communicating effectively.