Sand the surface of the river rock flooring using a sanding buffer and a medium-grit sanding disc. This will remove the varnish from the surface of the river rocks.
Sand the cracks and crevasses from the river rock floor using an electric hand sander with a medium-grit sanding belt. This removes the varnish from in between the individual rocks.
Vacuum the floor using a shop vacuum with a brush attachment to remove any dust and debris caused by the sanding.
Fill a paint tray with stone stain, any color, and coat a long-handled paint roller in the stain.
Roll the stone stain in an even layer over the entire floor using the paint roller.
Wipe a 2-inch flat paintbrush between the river rocks on the floor to spread any excess stain over the stones and out of the cracks. Allow the stain to air-dry for 12 to 18 hours.
Fill a second paint tray with clear masonry sealant and coat a long-handled paint roller in the sealant.
Apply the sealant over the entire river rock floor and allow the sealant to dry for 12 to 18 hours before use.