So i'm having two problems with this level. The first is how do you shoot the grates? I did it once but i don't remember what I did and I can't do it again. And the one time I was able to shoot the grates, i couldn't get across the river once the water level was raised. Is there a certain place to go across or a trick to it?

I use the crowbar to open the grates. On this level, use mouse aiming (alt key) and crouch right next to it. Enabling the crosshair (t key) helps a lot. After everything was under water on the left side of the river, I just ran across the river. You can run faster by pressing the shift key.