Multiproxy data collected from the largest inland wetland in Belize, Central America, demonstrate the presence of large-scale pre-Columbian fish-trapping facilities built by Late Archaic hunter-gatherer-fishers, which continued to be used by their Maya descendants during Formative times (approximately 2000 BCE to 200 CE). This is the earliest large-scale Archaic fish-trapping facility recorded in ancient Mesoamerica. We suggest that such landscape-scale intensification may have been a response to long-term climate disturbance recorded between 2200 and 1900 BCE. Agricultural intensification after 2000 BCE has been credited for supporting the rise of pre-Columbian civilizations in Formative Mesoamerica, but we suggest that some groups relied more heavily on the mass harvesting of aquatic resources. We argue that such early intensification of aquatic food production offered a high value subsistence strategy that was instrumental in the emergence of Formative period sedentarism and the development of complexity among pre-Columbian civilizations like the Maya.