Noise is definitely a factor underwater. A railgun is no different to any other, and it does make a noise. Fish are affected by noise but more so by the "pressure wave" that the rubbers put out when the gun is fired.
The pressure wave moves through the water at the same speed as the sound of the gun and with greater force. No matter how quiet you make the gun you still cannot eliminate the shock wave the rubbers will create when fired. Some divers put a neoprene sleeve around their standard barrel to try to silence it.
The problem with this is that the spear rests on it, therefore affecting the performance of the gun. The performance and "wet weight" of the gun will also vary at different depths because the neoprene sleeve will compress the same way your suit does. More.
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