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Not every plant is the same of course. Most aquatic plants have stomata. The difference between emersed and immersed plants is that there are no guard cells, so the plant pores cannot close. There's no need to retain water. Some plants with extremely thin leaves may not have stomata because there is no need for them. The gas in the water can diffuse directly across the membranes.

Lily pads may not have stomata on the underside of their leaves because there would be absolutely no point to them. The same reason we don't grow feet on our heads.
 
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