This is easier than you think
Woodland Scenics (http://www.woodlandscenics.com/) makes products that simulate water. They are very easy to use and can be molded/shaped to any form you want. Simply layout your river bed with rocks, dead trees and such. Set the banks as you wish. Prepare the woodlandscenics product, and pour. As the "water" begins to harden, give it a ripple effect around the rocks and such. It is really easy. Just visit their site or search for Model Railroading Sites they have a lot of experience with making rivers and lakes etc. Hope this helps!
Try this link (you may have to log in first!)
http://www.trains.com/Forums/MessageList.asp?messageid=674§ionid=88&threadid=106&sname=Model%20Railroading&threadname=First+time+%22water%22+maker%2Dbest+way%3F