I Went to Galapagos Islands for scuba diving liveaboard on Humboldt Explorer few years ago.
It was an amazing experience and I highly recommend it.
You can stay on some islands at resorts,hotels, hostels etc or as alternative you can take scuba diving or land-based cruises which cover several islands if you're not into scuba diving. Yes, for some of the islands you're prohibit to land on but others are inhabitant or open to visit.
Ecuador takes great care of this area and tons of wild life there.
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