Most visitors arrive expecting tropical heat all year round. There is a hot season in the Galápagos, but around May and June, as the trade winds pick up, two powerful cold currents arrive and change the diving entirely.
The Cromwell Current is an upwelling submarine current. It hits in the west, around Fernandina and Isabela. The Humboldt Current originates in the south, runs up the Chile–Peru coastline along the equator, and arrives from the south. Both enter Galápagos waters at 9–11°C (52–55°F).
Running against them, the Panama Current arrives from Central America at 29–30°C. That collision is the reason the equator is cold here — and the reason the nutrient upwelling it drives feeds the megafauna divers come for.
From June to October, expect water of 16–24°C (60–75°F), air around 20°C (68°F), and currents of 1 to 5 knots. Divers should be prepared for potentially strong currents.
Source: this post is drawn from a Travel eMOcean podcast conversation recorded on 1 July 2020 between Jenny Green and Jonathan R. Green.