Every time I walk by the pond near my house, there is always water in it. If I pour a glass of water on some dirt or sand, it sinks. Why doesn’t the water in the pond sink?
Sometimes it’s because it’s an intersection of the aquifer with the ground: in other words, the water’s already sunk as far as it will in this general region.
Other times, it’s located above impermeable rock and so cannot drain (quickly.)
I’m sure other times it does sink, like you said, just that the inflow matches the outflow, but I’m not sure how common this case is.
It’s a balance equation. Water coming into the pond > water leaving the pond.
Water leaves the pond by evaporation, percolation (what you describe), or by flowing through the outlet.
In a natural pond, a high groundwater level or impermeable soil can keep the water from percolating out; and/or sufficient water flows in to keep ahead of evaporation.
In a man-made pond, sufficient water flows in to keep ahead of outlet flow, percolation, and evaporation.
Different soils have different rates of percolation. Clays, for example, are extremely impermeable and are used for landfill liners as a result. Sand is extremely permeable (as you mention) and is not suitable for building of ponds. It does not take a large seam of sand in your pond bottom to completely drain it.
I think this is key.
When you pour water on the ground, the top surface of the ground is above the water table, so the water sinks into the ground. Most of the pond, OTOH, is probably below the water table.
Well, if you throw up a levee across a valley, you will catch enough water to overcome the amount percolating through the soil. So then you have what could be termed a ‘perched’ water table. But you created it when you caused water to pond behind the levee.
Mind you, in some areas this will not work, because the underlying soils are too sandy, or full of sand lenses and seams. In that case you won’t be able to hold water unless the groundwater level is high (or if you line the hole with Bentonite or other clays; or a synthetic liner).
A cup of water will sink in my clay soil. Five days of rain, though, makes it start to accumulate. When I get ready to sell me house, I have to time it very perfectly so that I can market it as water frontage.
You could go out there and seed it with Bentonite pellets. 
Occasionally lakes really do “sink”–see http://caveviews.blogs.com/cave_news/2005/05/disappearing_la.html for a couple of links to examples.
I once did see a real estate ad claiming that the property had a “seasonal waterfront”.