Merida is known more for its colonial charm and Mayan ruins than for waterways, but the city’s proximity to coastal and lagoon landscapes makes boat tours and cruises an ideal way to see the Yucatán’s natural beauty up close. Whether you’re into birdwatching, exploring mangroves, relaxing on pristine beaches, or snapping photos of flamingos in their natural habitat, Merida offers several unforgettable experiences. For instance, the Boat tour through the mangroves of Celestún from Merida (link) is a top choice, praised for its detailed wildlife encounters and small-group intimacy.
Many travelers love the full-day excursions that combine wildlife, beaches, and cultural highlights—like the trip to Las Coloradas and Río Lagartos (link)—which blend stunning pink lagoons with fantastic opportunities to see flamingos and crocodiles. Meanwhile, if you’re after a more luxurious or private experience, the Private Transfer from Merida to Progreso Cruise Port (link) ensures smooth, comfortable transportation for cruise travelers.
Quick Overview
This list covers a variety of boat tours and cruises catering to wildlife lovers, beach seekers, and cultural explorers. You’ll find options that include mangrove boat rides, flamingo safaris, lagoon visits, and full-day adventures. Whether you want a quick half-day or an immersive experience, each has its own special appeal. Now, let’s look at each one in detail.
1. Boat tour through the mangroves of Celestún and Playa from Merida
At number 1 is the Boat tour through the mangroves of Celestún and Playa, which scores a perfect 5.0 out of 5 from 62 reviews. This tour is a fantastic choice for nature lovers who want to maximize wildlife encounters in a small-group setting. The tour lasts about 9 hours, starting with an early pickup in Merida, and includes a boat ride that visits Bird Island, a crucial resting spot for migratory and local birds, especially flamingos during December through March, and Horseshoe Ruins—a quiet archaeological site.
What makes this tour stand out is its focus on birdwatching, with binoculars included, and the chance to see up to 100 flamingos in their natural habitat. The boat accommodates only 8 people, ensuring a personalized experience. The highlight is the visit to La Ramada de la tía Candi, where you can swim, eat a included lunch, and relax on the beautiful beach. Reviewers frequently mention the knowledgeable guide and the leisurely, unhurried pace that makes it ideal for wildlife photography and nature appreciation.
Bottom line: If you love birding and want a small-group, well-organized adventure, this tour delivers excellent value and memorable wildlife sightings.
2. Celestun Beach and Mangrove Boat Ride from Merida
Number 2 on our list is the Celestun Beach and Mangrove Boat Ride, a 10-hour trip rated 4.5 from 85 reviews. For around $114, you’ll take a boat cruise through the mangroves, scanning for crocodiles, raccoons, and a variety of bird species, including flamingos if the season permits. The guide is praised for their knowledge, making the trip engaging and informative.
The tour includes a relaxing stop at Celestun’s stunning beach, where you can swim, sunbathe, and enjoy the unspoiled blue sea. Its longer duration and focus on wildlife combined with beach time make it ideal for travelers who want a mix of adventure and downtime. Many reviews highlight that this is a fun, fast-paced ride with plenty of opportunities to see dolphins, rays, and birds.
Bottom line: Best suited for wildlife enthusiasts who want to combine a boat safari with beach relaxation, all at a reasonable price.
3. Las Coloradas & Río Lagartos with boat & Lunch from Mérida
Ranking third, this full-day tour (11-12 hours) takes you to the stunning pink lagoons of Las Coloradas and the diverse ecosystems of Río Lagartos, rated 4.5 from 31 reviews. The trip features guided visits to the pink salt lakes, a boat ride through the mangroves where flamingos and crocodiles are common, and a relaxing stop at the quiet Cancunito beach.
What makes this tour unique is the combination of spectacular photo opportunities in the lagoons, which are unlike anything else in the world, and the chance to explore mangrove ecosystems with a knowledgeable guide. The included lunch at a popular local restaurant is a welcome bonus after hours of wildlife and scenery. Reviewers often mention how the tour exceeded expectations, with many seeing about 100 flamingos.
Bottom line: Ideal for travelers wanting a comprehensive experience of colorful lagoons, wildlife, and quiet beaches, with plenty of opportunity for photos and relaxation.
4. Celestun Nature Reserve Flamingo Tour-Boat to Flamingo Paradise from Merida
Number 4 is the Celestun Nature Reserve Flamingo Tour, rated a perfect 5.0 by 4 reviews. This small-group tour focuses exclusively on the flamingo habitat, with a boat ride through the mangroves to see these striking birds up close. The tour includes lunch at a local beach and returns within about 8 hours.
What sets this apart is its intimate size and the emphasis on seeing flamingos in their natural environment—a must-do for bird enthusiasts. The guide provides informative commentary about the fauna and flora during the ride, making it an educational as well as scenic experience.
Bottom line: Perfect if flamingos are your main interest and you prefer a more exclusive, small-group experience.
5. Visit Bacalar full day with boat from Merida
Number 5 on our list is the full-day trip to Bacalar, rated 5.0 from 3 reviews. For around $150, you get a chance to see the Lagoon of the Seven Colors, take a guided boat tour across its shimmering waters, and visit Cenote Azul, Mexico’s deepest cenote. The tour is about 15-16 hours, making it a serious commitment but highly rewarding for those seeking a lagoon adventure.
Bacalar is renowned for its multi-shade waters and peaceful atmosphere. The boat trip offers a close-up look at the lagoon’s varying hues and the chance to swim in Cenote Azul. Many reviewers praise the scenic boat ride and the chance to relax on La Playita, a lakeside restaurant. It’s best suited for those willing to spend a day traveling, with plenty of time for swimming and photos.
Bottom line: An excellent choice for lagoon lovers and those willing to dedicate a full day for a relaxing, scenic escape.
6. Celestun mangrove boat tour from Mérida
The Celestun mangrove boat tour ranks sixth, rated 4.5 from 13 reviews. It’s similar to the first tour, emphasizing wildlife viewing within the mangroves, with a 2-hour boat cruise. The tour includes a visit to Bird Island and a final stop at a local stand for natural products or souvenirs.
This tour is ideal for travelers who want to spend less time on the water but still see plenty of wildlife, including crocodiles, flamingos, and raccoons. The group size tends to be small, and the guide’s storytelling enhances the experience. Reviewers mention the excellent guide and the opportunity to photograph flamingos and other birds.
Bottom line: Great for a shorter, wildlife-focused experience with a relaxed pace.
7. Excursion to Celestun, Swimming, Hiking & Boat Ride
At number 7 is the excursion to Celestún, rated 5 stars from just 1 review. This combines a boat tour in the mangroves, a beach stop, and hiking around the Horseshoe Ruins. The tour includes a 2-hour boat adventure and opportunities to swim and explore the area’s natural scenery.
This option suits travelers who want diverse activities—from wildlife watching to cultural exploration. The tour’s highlights include birdwatching at Bird Island, the estuary where freshwater meets saltwater, and the archaeological ruins. Expect a leisurely pace, with plenty of time at the beach and in nature.
Bottom line: Perfect for those seeking a mix of wildlife, beaches, and a touch of history.
$125.00 per person
8. Coloradas, Ria Lagartos Boat Trip & One Natural Beach from Merida
This tour ranks eighth, with no reviews yet, but it offers a full-day itinerary exploring Las Coloradas’ pink lagoons, Ria Lagartos, and Cancunito beach. It combines lagoon visits, mangrove boat rides, and relaxing beach time for a balanced experience.
Ideal for travelers keen on photography and wildlife, the tour allows you to see flamingos, lizards, and birdlife while enjoying quiet beaches away from tourist crowds. The inclusion of local natural beaches is a plus for those who want downtime.
Bottom line: A good pick for nature and photo enthusiasts looking for a comprehensive day trip.
$120.00 per person
9. Hike in Las Coloradas and Boat Tour of Río Lagartos
Number 9 is the Hike in Las Coloradas and boat tour of Río Lagartos, rated 0 reviews so far. This offers a guided tour of Las Coloradas’ pink lagoons and a boat ride through Río Lagartos. The tour emphasizes learning about the salt flats and the flora and fauna of the mangroves.
This is suited for travelers who enjoy combining walking with boat rides, and want to learn about the natural science behind the landscape. The tour includes photo stops and opportunities to see flamingos and crocodiles.
Bottom line: Great for those interested in educational nature tours with some light hiking and photography.
$115.88 per person
10. Private Transfer from Merida city hotels to Progreso Cruise Port
Last on our list is the Private Transfer from Merida to Progreso Cruise Port. At about 55 minutes, this service ensures comfortable, hassle-free transportation for cruise travelers. While not a tour, it’s a practical option for those needing a smooth ride to the pier, especially if you want to avoid long taxi lines or shared shuttles.
Rated with no reviews yet, it’s a solid choice for stress-free logistics rather than sightseeing. The door-to-door service and professional drivers make it perfect for cruise passengers who want to start or end their trip smoothly.
Bottom line: A practical, no-fuss service for cruise travelers needing reliable transport.
$134.13 per person
How to Choose the Best Boat Tour in Merida
When selecting a boat tour, consider your interests and time availability. Wildlife lovers and birdwatchers will enjoy tours like the Celestún mangroves (link) and Celestun Flamingo Tour (link), which focus on bird and animal sightings. Those wanting photo opportunities should look toward Las Coloradas (link) or Coloradas and Ria Lagartos tours (link).
For travelers on a tighter schedule, shorter mangrove tours (link) provide wildlife encounters in a few hours. Budget-conscious travelers might prefer the more affordable options like the Celestun boat tour or full-day trips with included meals and transportation.
Finally, if comfort and convenience matter most—especially for cruise passengers—the private transfer (link) is the best choice. Always book early to ensure availability, especially during peak season from December through March when flamingo sightings are at their best.
Final Thoughts
From wildlife safaris to pink lagoons and pristine beaches, Merida offers diverse boat experiences for every traveler. For nature lovers, the small-group tours in Celestún provide a chance to see flamingos and crocodiles without the crowds. If stunning scenery and photography are your focus, the Las Coloradas and Río Lagartos trip combines vibrant landscapes with wildlife encounters. And for those arriving by cruise, the private transfer ensures a smooth start or end to your journey.
Booking early is recommended, especially in peak season, to secure spots on the most popular tours. No matter your preference, this list helps you find a memorable water-based adventure in the Yucatán.