Look for a small place in Hamlet. Cliff is the house reef. We stayed there last year and enjoyed it. But we didn't dive much on it, so we skipped that this year. We're staying at a much cheaper place off the water.
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...A fun dive with BD&A - we did it even though we stay south - is their Naturalist led REEF fishcount. You get waterproof counting gear and the naturalist carries waterproof fishcards. Afterwards you compile your finds and send it in to REEF. Bari has one of the highest number of counted fish species in the Caribbean - I'm sure influenced by their operation...
I have only been to Bonaire twice, but have done a lot of diving in the Caribbean in general. My theory(just my 2 pesos) is that 2 bedroom units at dive resorts are not usually offered at great prices. Dive vacations with families or groups make the 2 bedroom units appealing and there is a big demand for those units. The first time my husband and I visited Bonaire we stayed at Bonaire Seaside Apartments. Units are sleek,and modern but are on the small side. The second time, we visited Bonaire, we booked a unit at Playa Lechi. This unit was pristine and more upscale from the previous place. However, it did cost more money. Literally next door was Dive Friends Yellow Submarine. They have a gear locker and platform for loading tanks into truck. Their house reef is good, but not in the league as Den Laman/Sand Dollar. The location of the above units was ideal. Quiet at night but a short walk to the restaurants in town. There is a one way road between the units and the ocean, but it did not obstruct with the views. When we return we will book at one of these units or neighboring Elagancia condos.