Deep-sea buoys equipped with thermometers recorded the warmest ever temperatures for a month of June.
The warmest waters were recorded in the Mediterranean of Tarragona, which reached 27C, an increase of 2.5 percent on a year earlier.
But the warm waters were not restricted to the Med. The temperature gauges also revealed rises in the Atlantic Ocean off Galicia, and the Bay of Biscay off Spain's northern coast.
Cabo Silleiro in the northwestern region of Galicia has registered a record of 19.9C – the warmest ever recorded, while off the coast of Bilbao, temperatures reached 23.5C in June.
Marine environmentalists have warned of the impact of warmer seas on marine life, encouraging invader species.
Spain was gripped by the first heatwave of the summer in June, making the month the hottest June recorded in Spain for 50 years.