It's been a slow-motion disaster and potentially catastrophic for two countries already burdened by major environmental challenges. The waters' rise has worsened exponentially in recent years, especially after heavy rains in 2007 and 2008 hit the island of Hispaniola, which both countries share. Tropical Storm Isaac dumped more water on the region in August, sparking more damage.
While the cause remains a mystery, theories as to why the lakes are rising range from sediment and trash clogging the water system to increased rainfall from climate change and heavy storms.
Dominican farmer Domingo Bautista recalls how the water gradually overtook his sugarcane, banana, and sweet potato crop. Within two months, the family had to abandon its one-bedroom home in the sunbaked village of Boca de Cachon.
The spread of Enriquillo has flooded 16 communities in two provinces, more than 46,500 acres of agriculture land, and 1,000 properties, according to a July study by the Technological Institute of Santo Domingo and the NOAA CREST Center of the City College of New York. In all, some 10,000 families have lost cattle, farmland, or their homes.
In Haiti, heavy rains made the situation worse last year and dozens of families were forced to evacuate. Many migrant laborers who cross into the Dominican Republic couldn't make the journey.
"It's a clear environmental disaster," said Antonio Perera, the Haiti country manager for the U.N. Environment Program. "It's happening slowly, slowly, slowly, and you won't see the immediate effects like an earthquake or hurricane."
Researchers have brought up several factors behind the rise of Enriquillo and Azuei, which both contain salt water because the low-lying region was once part of the ocean.
Scientists have speculated that, on the Haiti side, massive deforestation has caused sediment to fill the lake while trash clogs the canals that would drain it. The lakes in both countries may also be growing because of heavier-than-average rainfall in recent years.
On top of that, Perera said, Haiti's 2010 earthquake may have shifted faults beneath both lakes and somehow altered the hydrology of the area, though water levels began rising years before the quake.
"Two or three days after the earthquake there were springs everywhere in Thomazeau," he said, referring to a lakefront town on the northern end of Azuei he visited after the quake. "Even in the living rooms."
Lake Azuei has expanded outward by about three feet per year for the last 10 years, growing to 52 square miles, according to satellite images captured in the City College of New York study. It was once only on the Haitian side but extends across the border by one to two kilometers, covering a Dominican customs office in brackish water.
Similarly, Enriquillo's shores have moved out by about three feet per year over the last decade, reaching 128 square miles, double the size of the lake in 2004.
Many believe that the two lakes will soon merge as the water levels rise. Right now, they are separated by a road that often floods during heavy rainfall. Back-to-back storms in 2008 caused Azuei to spill and the border closed for several days, causing an untold loss in commerce.
Like Enriquillo, Azuei is surrounded by cinder-block homes, and even a two-story resort, that are either partially underwater or completely so.
Haitian farmer Cathleen Pierre and her family fled their home, now a part of Azuei, and live in a hodgepodge of shacks between the lake and the mountains. The high cost of living in Port-au-Prince makes sure they stay there.
"If the water rises again, we'll move farther up the hill," Pierre, 58, said as she hiked among her crops of corn and coconut. "We don't have another place to go."
Despite the obvious concerns, both governments have done little to stem the rising water levels or help the families displaced by them. And it's not clear what the countries plan to do in the long term.
Both sides are studying the phenomenon and have called upon the United Nations to implement a $2.5 million project that has planted thousands of fruit trees along the border.