Theres a good chance that deep water effects you can see from the side, like what you mean Ben, will still have a thin clear wall that holds it in. I think using a mould with realease would ruin the surface finish too much.
There's different approaches to prevent the "water" from running off the model. Like Klute said, some use clear plastic sheets/ acrylic glass and leave it in place permanently.
I've also read about using balsa wood (has to be removed before the resin fully cures though): water
Another approach that often is used on both model railroad layouts/ military dioramas is to use clear plastic sheets and non-hardening modeling clay (quoted from another forum, as it's a good summary of that method):
Here is what I normally do:
1. Get my hands on a clear plastic sheet. Overhead transparencies work really well for that. They are thin, flexible and resin will not stick to them.
2. Cut a strip long enough and wide (tall) enough so that it completely covers the gap (end of the river bed). In your case you will want to cut two of them. One for each end of your river bed.
3. Get some Plastalina. Plastalina is a non-hardening clay that you can get at any decent arts and crafts store. You will need to work it pretty well until it is soft and sticky
4. Position one of your plastic strips in such way that it is flush with the bottom of your base so that there is no gap. Then take the Plastalina and carefully stick it all along the edge of where the plastic sheet meets the base. Apply enough of it there so make sure it is air tight.
5. Now do the same thing to the edges of the plastic sheet. Make sure that they overlap the river banks a bit. Again, use plastalina to secure the strip.
6. Repeat this procedure on the other side of the river bed.
What you will end up with are two clear plastic dams. If you do this right, no resin will leak or seep through.
Haven't tried it meself yet, but like with everything else you probably should test it on something first before possibly ruining some nicely painted minis.