When I visited Devon last summer I got some pictures of the river Dart at Hexworthy.
- Use a commercial water product - but I've no experience of these, and the river is very shallow with a low lip at the baseboard edge - I'm not sure how well it would be contained
- Use gloss modge podge as I did for Loctern Quay - while this worked well for a painted "water" surface, any depth would take a lot of coats and I don't know how well it would dry if put on too thick
- Given the colour of the water in the photos above, good old yacht varnish might be a good bet. I used this on a layout I built in my teens, the main problem was it creeping up the banks which didn't look great.