Well in Marathon you "swim"
Think the swiming more like if the Marine has jetpack on his back to go out of the liquids because he weights to much, you can't really swim forward, but you can fake it pressing and releasing the swiming button at some interval. But hey, think about it, we're talking about a 9 year old engine, you couln't even get underwater in those old games.... heck, in Halo you can't go underwater.
Also you should check if you have always swim on as mitchellan said, if so turn it off (I'm not sure why the devs put this feature in, if you want autorun/swim you just configure the caps lock as your running key).