Repeatedly blow your whistle at Pikmin to drag them up onto land.

To keep your Red or Yellow Pikmin from drowning, have Blue Pikmin by the border. Do not have them selected. If a Red or Yellow Pikmin falls in the water near your Blue Pikmin, they will go to the Pikmin and throw them on land.

If your Yellow or Red Pikmin are drowning, quickly grab your Blue Pikmin and bring them into the water. Ungroup them and they will automatically toss the other Pikmin to safety. Note: You need to be near a ledge or the shore in order for this to work.

If you accidentally or intentionally put Red or Yellow Pikmin in the water, you can either press B and try to get them out of danger or you can put a group of nearby Blue Pikmin in the water near the suffering Pikmin and press X to deselect all of them. The Blue Pikmin should throw their fellow Pikmin out of the water towards land.

When your Pikmin are drowning, repeatedly press B to call them out of the water before they die.