Grenville's Planet (1952) by Michael Shaara, published in Urania #952 (1983).
The full text is available on the Internet Archive as a scan or transcribed. Extracts:
Grenville took the ship in close and now it occurred to him to wonder. That a planet should shine like that, like an enormous facet of polished glass, was incredible. Now, as he watched the light began to form vaguely into the folds of cloud. The blue grew richer and deeper. Long before he hit the first cloud layer, Grenville knew what it was. He pounded the buzzer. Wisher finally came.
When he saw the water in the screen he stopped in his tracks.
‘Well I’ll be damned!’ he breathed.
Except for a few scuds of clouds it was blue. The entire world was blue. There was the white of the clouds and the icecaps, but the rest was all blue and the rest was water.
Grenville began to grin. A world of water!
He was breaking the regs, of course. Since Grenville had not come back he must be considered dead and it was up to Wisher to leave alone. A special force would come back for Grenville, or for what was left of him. Wisher knew all that. He thought about it while he was loading the rifle. He thought about the vow he had made never to break the regs and he went right on loading the rifle. He told himself that he would take no chances and if he didn’t find Grenville right away he would come back and leave, but he knew all along that he was breaking the regs. At the same time he knew that there was nothing else to do. This was the one reg he had never faced before and it was the one reg he would always break. For Grenville or for anyone else. For a skinny young fool like Grenville, or for anyone else.
Before he left he took the routine precautions concerning the ship. He set the alarm screens to blast anything that moved within two hundred feet of her. If Grenville came back before him it would be all right because the alarm was set to deactivate when it registered the sound pattern of either his or Grenville’s voice. If Grenville came back and didn’t see him, he would know that the alarm was on.
And if no one came back at all, the ship would blow by itself.
For the ship had been seen from the very beginning, and its purpose understood. The best brains of the sea had gathered and planned, the enormous, manta-like people whose name was unpronounceable but whose technology was not far behind Earth’s, met in consultation and immediately understood. It was necessary to capture the ship. Therefore the Earthmen must be separated from it, and it was for this reason that Wisher had died.
But now, to the astonishment of the things, the ship was still alive. It stood silent and alone in the whiteness of the beach ticking and sparking within itself, and near it, on the bloodied sand, were the remains of the one that had come too close. The others had fled in terror.
Time was of no importance to the clever, squid-like beings. They had won already, could wait and consider. Thus the day grew late and became afternoon, and the waves - the aseptic, sterile waves which were proof in themselves of the greatest of all oceanic civilizations - crumbled whitely on the beach. The things exulted. The conquest of space was in their hands.
Within the ship, of course, there was ticking, and a small red hand moved toward zero.
In a little while the ship would blow, and with it would go the island, and a great chunk of the sea. But the beings could not know. It was an alien fact they faced and an alien fact was unknowable. Just as Wisher could not have known the nature of the planet, these things could not now foresee the nature of the ship and the wheel had come full circle. Second by second, with the utter, mechanical loyalty of the machine, the small red hand crept onward.
The waves near the beach were frothy and white.
A crowd was forming.
Found by searching this site for
[story-identification] astronauts water which led me, among others, to Collection of sci-fi/fantasy short stories: tiny aliens crashlanding in a backyard on Earth, growing a star as a school project, and some Le Guin, this story in particular sounding interesting:
There was one I only vaguely remember about a planet that was 99% water with only a few islands. I think some astronauts crashed there and had to find a way off?
Then I proceeded to look up the various stories in the anthology given as the answer, and Grenville's Planet was it.