Pump the water out and refill it, while having a filter set up too. It's possible to make a home made filter utilizing the pump and a 5 gallon bucket, you'll have to google the specs since I only have a general idea of it.
The other option is to build it above ground and install a drain. Make the drain with a hose attachment nozzle on it so that you can connect a hose and direct the water where it would not be an inconvenience. Or move it around the yard as a lawn watering system. I have a small pool, so I just pick a new spot in the yard to water every day. Mine is elevated just enough on the gravel base of the run to allow for natural suction. Takes awhile, but I have two hoses, I run water into the pool to fill the hose, go over to where the hoses connect, and I have this handy-dandy shut off valve incorporated into the connection (bought it) and I shut off the water, unscrew the hose (while keeping it very low to the ground since I only have about 8 inches of elevation on the pool, I can't really lift the end of the hose more than 8 inches off the ground)
That causes the water flow to reverse itself, and it drains the pool without a pump, and through a hose so I can choose where it goes instead of flooding the run.