Don't you hate it when you have an transport network and you need to build a tunnel underwater due to the fact that making a train route on the bridge right above it would clog up the whole system? Well my suggestion is to make it so you can landscape the terrain a block way from water so it can go below the water level (In other words, be able to terraform land down to the -1 mark without water stopping you). So please take this into mind. Thanks!
Someone has done some work on varying water levels. But I've never had any troubles with tunneling under water due to the water level. I also think real under water tunnels tend to start above the water level.
I never found a way to tunnel underwater even though I've tried and tried to make the level of the tunnel go down. One reason why may be that I'm kind new to Simutrans and don't really know all that much. :P
There is a tutorial here: http://forum.simutrans.com/index.php?topic=3716.0
If you start the tunnel a bit further from the shore, you don't have to make the boxes in step 2 that needs to be repaired in step 8.
Thanks ;D