Hi Matt.
That is starting to look interesting.
I would add the wooden fenders before you add any more surfacing to the water so that you can get it all blended in together.
On our St Mellion layout I used Winsor and Newton Galleria acrylic paint mixed with other acrylics to get the water colour. I had several goes at it before I got it to look right. This comes in a tube or tub and is relatively thick. So if you apply it with a wide flatty brush it will stand up a little and you can create a wave effect. I then applied several coats of yacht varnish using the same technique to build up the clear water effect.
I hope that this is of interest.
All the best
Ray
P.S. You might remember the centre warehouse building as one that Mick Foster built for one of the early club layouts. It is now on its third layout ! Mind you, I had to repair it quite a bit and re-paint it, but it is still quite fragile.