I think you will want to dig enough to scrape as much topsoil off the site and store someplace else if possible. This could be a few feet of materials off of the pond basin or more. This would be to simply remove organics that may lead to algae and plant problems from the beginning and result in clearer water and lengthen the natural aging process of the pond. It may also expose sand and gravel veins that would need to be addressed with clay that otherwise may result in leaks.

With such shallow contours, a dam across just the stream may not be enough to address all of the paths the water may go once it starts backing up. It is also nice to have a few good, deep spots that stay cool during hot weather.

Bear in mind, this is my un experienced opinion, I am no expert. However, I am getting the itch to find property which supports a much larger pond, and have observed construction of a pond in a very similar situation as yours. They had to ring 1/3 of the downstream side of the pond with a core dam to address all of the old stream beds made of gravel and sand to hit clay below. Otherwise it would simply not hold water.