You might want to re-think using varnish (if it really is varnish and not urethane) for water, and even as a coating, it's not the best choice. Most true varnish yellows with age, and if you're thinking of pouring it to some depth, chances are it will crack, as it's not intended to be used in that manner.
I think that Realistic Water would be a better choice: if price is a problem, don't fall into the trap of thinking that your "water" has to actually be deep - the trick is to prepare the surface (harbour floor, in your case) so that a thin layer of the Realistic Water will make it appear to be deep.
I used an alternative method, creating the "water" using Durabond 90 patching plaster. In most areas, it's only 1/8" thick or so, although in one scene it's over an inch deep. I buy it in 33lb. bags, as I use it for my basic landforms, so it's not very expensive to use it for water.
After the plaster cures (it sets in 90 minutes, but I left it for a couple of days), I brush-painted it with interior latex house paint, adding white water effects with a small brush and some PollyScale Reefer White. After the paint had dried for a few days, I brushed on three coats of water-based high gloss clear urethane, allowing the suggested drying time between coats. It's been in place now for several years, with no yellowing, cracking, or scratches, even though cameras are often placed directly on its surface.
And don't think that just because something "is there, it is there". Anything on a model railroad can be changed: you need only the reason to do so. Believing otherwise is one of the things that causes people to not accomplish the things which they want, because they're afraid to fail. I have failed many times, but I've also learned, through those failures, how to be successful too.
Wayne