This is how you could make submerging tunnel.
1st.

Find a river(i suggest a small river that wouldn't cost much diamonds)
2nd.

make the road with tunnel capabilities start from two tiles away from the river side. 3rd.

Make tunnel across the river (doesn't need to be finished, just make the tunnel entrance and make sure its 1 tile away from the river side. And then, its your submerging tunnel... Cars should enter water to cross the river... Xd

