As I was researching some articles this morning I found that a large majority of studies that were comparable to ours in terms of the overall goal used aerial photography. These studies said that it was a costly yet accurate method. Other studies used the perspective tool in GIMP and photoshop but were unsure how accurate that method was.
After exploring some software I found that it may be more helpful (especially with the many that deal with 3D imaging) to take pictures of the streams first so we have objects in more than one dimension.
I did find one study that seemed like it would be a great resource for us to use in terms of methods and analyzing data. The link is below but I will read more about it and share anything that seems relevant.