The flower clouds are flower-shaped clouds that appear in the sky in almost every episode of the series.
The clouds appear in the sky and come in various colors. When in Bikini Bottom, they appear normally, but when outside of the town, they appear stretched out and distorted. They are able to fall from the sky, as seen in The SpongeBob Movie: Sponge Out of Water. They are Bikini Bottom's version of clouds.
It is possible that the flower clouds are actually flowers, without stems, that somehow fell on top of the ocean.