The only natural lake of any size in the country is Lago de Yojoa, 16 kilometers long by 8 kilometers wide at an elevation of 635 meters. With the construction of El Cajón dam, a larger man-made lake was created along the Río Humuya.

On the north coast, and particularly in the Mosquitia, are many lagoons and freshwater wetlands, separated from the ocean by narrow sandbars. Among the larger lagoons are Laguna de Alvarado behind Puerto Cortés; Laguna de los Micos, near Tela; Cuero y Salado, just west of La Ceiba; and Laguna Guaymoreto, outside of Trujillo.

Farther east in the Mosquitia, these lagoon systems are much more extensive. The largest is Laguna Caratasca, measuring 66 kilometers long by 14 kilometers wide and linked by waterways to the adjacent Laguna de Tansin and Laguna de Warunta. Other large lagoons in the Mosquitia include Laguna de Brus and Laguna de Ibans. In fact, one could reasonably consider the entire Mosquitia coastal area one huge wetland system, as networks of canals and seasonal waterways extend basically from the Río Coco all the way to Palacios.