The most important river in Honduras is the Ulúa, which flows 400 kilometers to the Caribbean through the economically important Valle de Sula. Numerous other rivers drain the interior highlands and empty north into the Caribbean. These other rivers are important, not as transportation routes, but because of the broad fertile valleys they have produced. The Choluteca River runs south from Tegucigalpa though Choluteca and out at the Gulf of Fonseca.

Rivers also define about half of Honduras's international borders. The Río Goascorán, flowing to the Gulf of Fonseca, and the Río Lempa define part of the border between El Salvador and Honduras. The Coco River marks about half of the border between Nicaragua and Honduras.

Despite an abundance of rivers, large bodies of water are rare. Lago de Yojoa, located in the west-central part of the country, is the sole natural lake in Honduras. This lake is twenty-two kilometers long and at its widest point measures fourteen kilometers. Several large, brackish lagoons open onto the Caribbean in northeast Honduras. These shallow bodies of water allow limited transportation to points along the coast.