The Garua Season is at its peak now making September (and August) the coolest and driest months in Galapagos (though still pleasant with highs of 24 °C and lows of 19°C). Seas are also cool and fairly rough in these months.
The ground in many places is rock hard, making it difficult for terrestrial birds such as finches and mockingbirds to find seeds and water, however life at sea is now plentiful as the Cromwell Current and South Equatorial Current, the cold water currents that bathe Galapagos are in full effect which means nutrient-rich water is brought to the ocean surface, making marine life in the Galapagos very active.
One of the highlights of snorkelling at this time of year is the good chance of swimming with sea lion pups. September also has higher chances of seeing whales and dolphins when navigating (along with July and August).
Sea bird communities are very active thanks to the abundance of food for marine life. The Albatross chicks have by now grown large and fluffy and are often left to fend for themselves as their parents head out to sea to look for food. One advantage of September, is that because many tour boats go for their annual repairs now, September is a relatively low season and as a result you get less people on the trails.