Great site, been looking for something like this. Thanks
Are you talking about building a dam? Altering the natural hydrology can really have unforseen outcomes. Sediment loading alone can create major changes (Erosion) downstream. The professions most skilled at figuring out these complex interactions may be in the engineering fields: hydrogeologists, for example. Large scale water manipulations require skill and experience beyond what you will be able to get from a forum like this. I would suggest you find a professional who has proven experience.
Sorry, I can't help it. Every time I hear the word pond I think;
See Josh's link for bentonite products.