JDD, groundwater comes out of the ground like from a spring, well, etc. Runoff is surface water; what runs on top of the ground, in streams, etc. The area of land uphill of your pond that will drain rain water into your pond is called the watershed. The pond area actually covered with water is called the pool area.
If you line the pond with well compacted clay, you seal off all groundwater except for the most minor of seepage. In a clay lined pond, the water will have to come from rainwater runoff, springs upstream becoming surface water, or a well.
Depending on the soils within the pond and immediately surrounding area, and the dam location, clay is "tied in" when compacting a core after digging a core trench down to good clay and onto the hillsides for the "toe'" of the dam. A builder will dig and look for good clay soils that cut off gravel seams, sand veins and other permeable substrates below the projected pool level. It is possible that the pond itself may not even need to be clay lined, but if it is lined, there is no real need to tie the uphill clay into the soils since water does not drain out uphill. Depending on your particular topography, watershed and soils, a clay liner only needs to extend above the full pool level a foot or two in order to prevent erosion in large rain events that will raise the pool level until your spillway system can drain the excess water away.
I am sure Mike Otto's new book, "Just Add Water" would explain this much better and provide you with many details on what to look for and do when building your pond.
