On this small island, most of the Bonaire snorkeling accommodations are in or near Kralendijk. If you are wondering where to stay for access to the snorkeling, it does not really matter as you will be driving anyway.
There are beach resorts, dive resorts, bed & breakfasts, apartments/condos and vacation rentals available. Having a kitchen in your unit is common on Bonaire. Some waterfront accommodations have snorkeling directly from their property and though you will likely see fish, most of it does not have live reef, with the exception of staying on Lac Bay.
In Kralendijk there are some hotel style beach resorts like Divi Flamingo Beach Resort and Casino, Plaza Resort and Harbour Village Beach Club. Of these, the best for direct snorkeling is Plaza Resort at 18th Palm, described in our eBook. One benefit to these resorts is that they also have restaurants. In town there are also apartments near or on the waterfront like Bonaire Seaside Apartments, which are easy walking distance to restaurants.
On the north end of town there are a series of dive resorts like Buddy Dive, Hamlet Oasis, and Eden Beach Resort. In this same area there are some waterfront condos like Sand Dollar Condominium Resort and Den Laman Condominium. Though you can snorkel from all of these accommodations, we think the best are Hamlet Oasis for Cliff, described in our eBook, and Den Laman for Bari Reef. Many of these places have on-site restaurants.
In Belnem, south of town past the airport, there are some waterfront apartments like Belmar Oceanfront Apartments, Bellafonte Chateau de la Mer and Happy Holiday Homes. In this area there are also Bed & Breakfasts like Oasis Guesthouse. Staying in this area requires a drive to get to the restaurants in town.
On Lac Bay on the east side of the island there are two beach resorts Sorobon Beach Resort and LacBaai. With a long walk in the water, you can access great snorkeling from Sorobon Beach Resort. These accommodations provide restaurants and there are snack bars and another restaurant on Sorobon Beach.
If you are looking for more affordable non-waterfront options look for apartments like Yacht Club Apartments or BonaireFun Appartments. A couple more affordable dive oriented accommodations are The DiveHut and Caribbean Club Bonaire.
You could also book yourself a vacation rental. They come in all sizes and price ranges. TripAdvisor has many options available.
The more in town you stay the closer you will be to restaurants, which are primarily in Kralendijk. Be sure to bring mosquito repellent to outdoor restaurants in the evenings.
The restaurants on Bonaire are pretty expensive, so we lower the expense by doing some cooking for ourselves, and the grocery stores are well stocked to do so. Most of the large grocery stores are on Kaya Industria. The newest one is called Van Den Tweel and in our experience was great, but many of the labels are in Dutch, so there is a learning curve. Grocery stores do not supply bags, so bring your own, or pay for a reusable one. Sometimes your apartment will have some you can use.
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