Multiple realities(covers information from several alternate timelines)
A water landing was either a controlled landing or a crash landing in a body of water.
In an alternate 2259, the USS Enterprise commanded by Captain James T. Kirk engaged in a water landing on Nibiru, where it submerged itself under water much like a submarine, so as to keep hidden from the planet's inhabitants while they were there. (Star Trek Into Darkness)
In an alternate 2263, the USS Franklin, under the command of Captain Kirk, crashed into the large body of water surrounding Yorktown Central Plaza. (Star Trek Beyond)
In 2269, Aqua-shuttles were used for water landings and underwater missions. The crew of the USS Enterprise took an Aqua-shuttle to Argo for such a mission. (TAS: "The Ambergris Element")
In 2286, the Klingon Bird-of-Prey known as the HMS Bounty crash landed in San Francisco Bay, forcing Kirk, his crew and George and Gracie to abandon ship. (Star Trek IV: The Voyage Home)
On the planet Ba'ku in the year 2375 after jumping out of the airlock of a holoship into the lake below, Data informed Captain Jean-Luc Picard and Anij that "In the event of a water landing, I have been designed to serve as a flotation device." (Star Trek: Insurrection)
That same year in the Delta Quadrant, Tom Paris modified the Delta Flyer for underwater travel and made a water landing on a Monean planetoid. (VOY: "The Voyager Conspiracy")