Clean off the concrete base of the shower to remove any loose debris using a vacuum or dust broom and pan. Just as if you were laying tile, you cannot use a fiberglass shower base since the mortar will not adhere to it. Unscrew the drain cover with a screwdriver and set aside to replace later.
Trowel on a layer of thinset mortar using a one-quarter-inch notched trowel. You can use ready-to-use thinset or mix your own in a bucket. The base of a shower will not require very much thinset, so only make as much as you can use in 30 minutes.
Set evenly sized pebbles into the thinset, each with a small one-sixteenth-inch gap from the other. Press each stone slightly to make sure there is good contact between the pebble and the thinset. Lay stones carefully around the drainpipe, keeping them just below the surface so that the drain cover will still fit easily. Wipe up any thinset that squeezes out to the top of the pebbles with a damp rag. Dry the thinset overnight.
Apply grout with a color that complements the coloring of the pebbles. Use a float to press the grout into the areas between the pebbles, working on one small area at a time. Wait for a few minutes for the grout to harden slightly, usually about 10 minutes.
Use a large sponge to lift off the excess grout from the surface of the pebbles, rinsing the sponge often in clear, cool water. Dry the grout overnight.
Scrub the pebble shower floor with a stiff-bristled brush and water to remove the haze from the surface of the pebbles. Wipe dry. Allow the grout to continue drying for 48 hours.
Seal the grout with a grout sealer to keep the moisture from the shower penetrating the grout. Apply the sealer liberally, adding more until the liquid no longer seeps into the grout after 10 minutes.
Screw the shower drain cover back in place with a screwdriver. Dry for at least three hours before using the shower.