Book your tour with a company that follows ecotourism rules and guidelines and makes every effort minimize impact on the environment. Talk to company representatives ahead of time about efforts they make to minimize impact.
Make sure that the company you travel with has a goal of environmental education. Tours in the Galapagos should include education for tourists about the wildlife and the intrinsic value of the natural landscape.
Stay with your guide at all times when on the islands. While there may not be a designated trail, follow your guide so as to avoid walking in places off the guide's path. Guides should choose a path that is least threatening to the natural state of the island.
Conserve the resources on your boat such as water and electricity, and refrain from camping on the islands even when government regulations allow it. Camping has a more serious affect on the islands than staying on a boat at night, and because of the delicate ecosystem it is not recommended.