Military sonar is probably the biggest offender. Obviously, it's going to be pretty hard to get the USN to abandon sonar altogether. However, perhaps there are ways they could modify operating procedures to reduce the impact on marine life. Whales surely show up on sonar, so it would make sense to reduce ping volume when they are near whales in non-combat situations. Focusing on more sensitive microphone technology might allow the Navy to use weaker pings without compromising range. Passive listening techniques, such as those used by submarines, could probably be used to a greater extent on the surface too. Quieter propellers, outboard pickups (probably already in use), or simply stopping when using sonar might also permit the use of lower volume pings. All that is really needed is for the Navy to make lower noise one of their design priorities.
Likewise, commercial traffic probably considers fuel efficiency to be top priority when designing propellers, etc.. Quieter propellers are probably less energy efficient, so regulations would likely be required to encourage commercial ships to reduce their noise emissions.
I could be wrong here, but I think quieter propellers may be more energy efficient. Since noise is just energy, it's wasted on noise rather than propulsion. Case in point: Formula 1 engines this year are turbo, and are much quieter. Many fans complain because they are too quiet! But they are more efficient.
This article piqued my interest so I googled for recordings of underwater sounds. Here is a gallery of underwater audio clips from various mammals, invertebrates and more: http://www.dosits.org/audio/agsummary/
Likewise, commercial traffic probably considers fuel efficiency to be top priority when designing propellers, etc.. Quieter propellers are probably less energy efficient, so regulations would likely be required to encourage commercial ships to reduce their noise emissions.