Been to Bonaire a couple of times now and only done shore dives (due to time limits with work) but they have all been very worth while. It seems like it doesn't matter where you dive here, you'll find an ambundance of life. One of the sites was at a dive resort called Buddy Dive, another from a hotel called Plaza and the third a quiet beach down the road.
All sites were similar due to being withing 1 - 2 miles of each other but was not disappointed at all. Managed to see many, many different fish, Tarpon, Squid and lots of different coral. Can't wait to get back with time to do some boat dives!
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I always think that when shore dives are in good condition it bodes well for the off-shore ones!