A lot of people don't know it, but the Galapagos can be done independently.
There are small boats every day between the 3 bigger islands of San Cristóbal, Santa Cruz and Isla Isabela. They cost $40 one-way, but some people have got them for $35 when they ordered a return-ticket with an open return date. From these island you can do organized daytrips, but there are also a lot of things you can do on your own.
There are hotels and hostels on most of the islands ranging from $35-$500+ which often do not need to be booked in advance. Many hotels and hostels arrange day tours. However, most tour agencies operate on Santa Cruz Island around the waterfront where day trips of all kind are offered.
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