Xaniel
I assume the river is the lowest area on your layout. Fake (ie model) water doesn't really need any depth - the illusion of depth is created with colour. The darker the colour, the deeper we perceive the "water" to be. So, the depth you have allowed for the river is not really needed.
The first thing you want to do is detail the banks. I've had great success with spackle, Poly Instafill is a good one, comes pre-mixed, dries fast etc. I'm not too careful when I put it on, cuz I like some of the cool things that happen where coverage is uneven.
Next, paint the river bed. Some modellers use almost black paint in the center which is the deepest part, and graduate it to a lighter earth colour at the edges. How dark you make it depends on how "deep" the water is. For a shallow stream the colour would be lighter than say a deep harbor. Then apply a few rocks (real pebbles are free and very realistic!) - some flat ones that will be visible through the water and some that actually show above the water level. Here's where some good reference photos come in handy.
An excellent source for reference photos are stock photo agencies used in the graphics biz (that's my background). Try
www.eyewire.com - type in the word "river" hit the search button and voila! The only thing you need to know is that these images are copyright and you're not allowed to reproduce them - ie on a webpage - without paying. But if all you want to do is see what something looks like, it's really useful.
There are some online clinics on making rivers and ponds too. I really liked this article from MRR magazine:
http://www2.modelrailroader.com/content/dynamic/articles/000/000/002/504xisqm.asp
Hope this helps.
Cheers
Val
Can you believe this is a MODEL???!!!!! (Image from MRR online)