This dissertation focuses on a little-explored system of freshwater wetlands in the northeastern Yucatán Peninsula of Mexico. Previous archaeological research at one wetland in the Yalahau region found evidence for manipulation in the form of constructed rock alignments, which likely functioned as dikes and dams to control soil and water for food production. There are 175 wetlands in the Yalahau region, therefore the goal of the regional survey was to assess the extent of wetland manipulation, and correlate this manipulation with wetland environmental variables such as vegetation, topography, soil type, and flood regime. A sample of 25 wetlands was selected for survey. Fieldwork involved vegetation mapping, rock alignment mapping, plant collections, topographic transects, installation of water loggers, and extraction of soil cores. Using these data, I evaluate hypotheses regarding patterns in the distribution of alignments, chronology of wetland use, and relationship between developed wetlands and nearby ancient sites. My research shows that wetland manipulation with rock alignments was widespread in the Yalahau region, and that the Maya tended to build rock alignments in very particular physiographic contexts. This project provides a basis for future investigations into rock alignment function and how the Maya adapted to changing environmental conditions in the wetlands.