bldean,
NO you cannot use roundup in your pond to control any plant. It is not labeled for aquatic usage. However, there are aquatic approved herbicides which utilize glyphosate as an active ingredient. They are sold under the trade names rodeo, eraser AQ, shoreklear plus and others. Glyphosate herbicides can be a good herbicide to control water lilies. They should be applied directly to the leaf of the plant. Glyphosate herbicides are systemic and act by moving through the plant and killing the root or in this case rhizome.
I personally prefer to use a 2,4-D aquatic herbicide for control of water lilies. The one I use is navigate.
For mixing just follow the label of the herbicide and add a aquatic approved surfactant if needed (rodeo).
Here is a link to aqua plant for more information on herbicide control:
http://aquaplant.tamu.edu/management-options/white-water-lily/