A 3 m core from the New River Lagoon, adjacent to the Maya city of Lamanai, Northern Belize, contains a continuous record of vegetation change between c. 1500 BC and AD 1500. Inferred changes in forest abundance and plant community assemblage build on previous palaeolimnological analysis of the same core reported by Metcalfe et al. (2009). A near-complete, abundant record of Zea mays grains provides a detailed account of field-based agriculture local to Lamanai, in the context of a regional record obtained from a large lake (13.5 km2) with a substantial catchment. Three periods (c. 170 BC–AD 150, c. AD 600–980 and c. AD 1500) of extraction of Pinus from pine savannas adjacent to the east of the New River Lagoon, can be distinguished from clearance of seasonal broadleaf forest for agriculture. An increased palm signal is observed during c. 1630–1150 BC and 100 BC–AD 1100 and may be indicative of Maya cultivation. This record shows that during the late Classic period the Maya actively managed the vegetation resources using a combination of field-based agriculture, arboreal resources and perhaps, palm cultivation. There is no evidence from the vegetation history of drying during the late Classic coincident with the Maya ‘collapse’ and this is consistent with the palaeolimnological and archaeological records of continuous occupation of the Maya at Lamanai. Both the decline in palms c. AD 1400 and the increase in Pinus extraction c. ad 1500 are consistent with changes in vegetation associated with European arrival, however further analysis of material from the last 1000 years will enable a better understanding of vegetation change pre- and post-European encounter.