They don't spawn in the water they spawn in the air surrounding and fall into the water getting pushed away. Once they reach far enough away the spawner will spawn more mobs.

Can mob spawner mobs spawn on water?

Mobs can't spawn in water, even from Monster Spawners! The special rule of spawners is that they can spawn mobs in midair; their spawns still require appropriate (lack of) lighting and an empty space, but they do not require an opaque block underneath like normal monster spawns do.

Will mobs spawn in water?

Mobs other than water mobs are unable to spawn in water. Mobs other than striders are unable to spawn on lava. (Side note: You can download mods to show where you have to spawn-proof for your mob farm or entity removing needs.)