Beachcomber (1952) by Damon Knight, available at the Internet Archive; publication history at ISFDB.
The Beachcomber made an impatient gesture. "You don’t think we could bring it back into a space it already occupied, do you? It was in stasis, all but a fraction out of this time-line. Just a miniature left, so that it could be controlled. A model of the universe, so big." He spread his thumb and forefinger an inch apart — "Just a pebble."
Maxwell's jaw dropped open. He stared at the giant. "You don’t mean — you — "
"Oh, yes," said the Beachcomber, "I landed about twenty miles out from shore — five years ago." He stared out across the sea, while his fingers groped nervously among the pebbles at his feet.
"And when I hit the water," he said, "I dropped it."
I remembered that this had appeared on the site before, so I searched for site:scifi.stackexchange.com short story man searches for world lost on beach, which brought me to Short story: pebble-sized galaxy lost on a beach