Firefighters said two of the dead were fishermen in Manta, who went missing on Friday and were found lifeless on Saturday.
The beaches in that city in Manabi province have been closed as a precaution.
The other dead man entered the sea in La Libertad district, in Santa Elena province, and was swept away by the waves.
Images shared on social and local media show how beach huts and shops were destroyed by the waves.
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