Stream construction question

I'm putting in a short, minimally sloping (1/4" / ft) stream for a new
pond. Rather than try to shape the stream bed when I dig it, I though
I'd just dig a trough with a constant slope and width, put in the
liner, and shape the course of the stream with river rocks and sand.
In order to make dams along the way so the stream doesn't drain
completely when the flow is off, I'm wondering if clay, protected by
the rocks and sand, would work. Any comments?

Chris