Shut off the well pump. If your well does not have a shut-off at the well head, turn the breaker that supplies power to the well to "Off."
Open the valve to drain the holding tank. Use a wet-dry vacuum to siphon out any water remaining once you've drained the tank.
Mix a solution of ½ gallon of bleach to five gallons of water, and use this to scrub out the holding tank. Rinse the tank and vacuum dry again.
Add three pints of bleach to the tank for each 100 gallons of water it holds. Close the tank and restart the well. Allow the holding tank to fill with water. The bleach in the tank will kill the bacteria in the water.
Refrain from using the water in the well for at least two hours (and preferably overnight.)