In Yucatán there are no true rivers above ground, only formations called rías, which are entries from the ocean to the coast, forming canals with abundant aquatic vegetation called mangroves. It is worthwhile exploring them; it is a unique experience. Declared “Biosphere Reserve,” with 60,000 hectares, Ría Lagartos, located 2.5 hours from Mérida (230 kms) and from Playa del Carmen, and 1.5 hours from Chichén Itzá, hosts the largest American flamingo population in México. They build their nests in the spring and summer. Its coastal lagoons are areas of seasonal rest and winter territory for flocks of migratory and local birds, with a current record of 388 different bird species in the area. The beaches offer habitat for nesting of Carey and white marine turtles.
The cooperative Río Lagartos Adventures is led by Diego Nuñez, naturalist and birding and fishing guide. The cooperative offers bird watching by boat and on land, Flamingo tours, crocodile night tours, and sport fishing / fly fishing. Diego Nuñez pioneered eco tourism in Río Lagartos. The cooperative is made up of the Nuñez, Marfil, Canul, Contreras, and Vallejos families, 100% local people. They are located at the RIA MAYA RESTAURANTE AND POSADA, where they have comfortable boats, kayaks, mountain bikes, and trained & certified guides, ready for you to enjoy the various tours offered in English, Spanish, or Italian. Río Lagartos Adventures offers nature tours, with 20 years experience guiding trips in the Ría Lagartos bio-reserve. Their 3 most popular tours are: boat tour to observe flamingos, night tour to observe crocodiles, and bird-watching tour (boat or land). www.riolagartosadventures.com Reservations: Cel. 9861 00 83 90. or www.riolagartosnaturetours.com 
The RIA MAYA RESTAURANTE AND POSADA is located at Calle 19 No. 134 x 14, on the waterfront. Cel. 9861 00 83 90. You can also enjoy delicious seafood here, and with their second story palapa roof terrace, it's the best spot to watch the sunset. The four-room posada has been recently renovated. To find them: you will enter Rio Lagartos on the main street. As you cross the 4th speed bump (tope) turn to the left. There is a sign. Follow this street (Calle 19) and it will bring you directly to them (on the waterfront) at "Ria Maya Restaurant and Posada" (formerly Isla Contoy restaurant).
For detailed information about the flora and fauna of the area, visit Jim Conrad's Backyard Nature site , where if you take the time to explore, you will find postings which specifically relate to Río Lagartos.
Extremely Rare Video of a Jaguar at Night in Rio Lagartos, Yucatan
See phots and video here: http://youtu.be/K-k3L5JgXps 
How to get there :
You can get to Río Lagartos via a travel agency, in a rented car or by bus. By car from Mérida drive east to Tizimín and then go north to Río Lagartos.
San Felipe is a quaint fishing town, 9 km. west of Río Lagartos.
Hotel in San Felipe:
- Hotel San Felipe
9 km. west of Río Lagartos
Tel: (986) 862 2027
Email: [email protected] 
Río Lagartos is within the Biosphere Special Reserve and it's famous for its enormous flamingo colony and large variety of other species.