I mention this above in my own comment, but a railgun would instantly vaporize the water it comes into contact with. If you look at the footage and pictures of the US Navy's railgun tests you will note fire around the weapon barrel when it is discharged. Railguns don't use explosive propellant, that is the AIR catching on fire from the friction against the projectile.
Not all air, there are materials that are shearing off the rails and projectile turning to plasma. It's important to not just think about throwing a modern railgun under water and firing it, we all know what would happen there. But instead what happens when a railgun is specifically designed to work submerged including the use of advanced (even alien) technology. Things make more sense that way.
I don't care how much tech you have, when something moving at the kind of speed achieved by a railgun hits the water the proverbial shit is going to hit the fan.