We inferred environmental changes in the northern Neotropics using geochemical and mineralogical data from the sediment record of Lake Petén Itzá (Guatemala), covering the Marine Isotope Stages (MIS) 3 (57-29 cal ka BP) and 2 (29-15 cal ka BP). Our study focused on past changes in runoff, lake evaporation, organic matter sources and changes in redox conditions associated with water-level variations. Wet conditions, higher primary productivity and anoxic bottom waters were inferred for MIS3. The transition from MIS3 to MIS2 (39.0-23.0 cal ka BP) was characterized by increasing lake evaporation and oxic bottom waters, possibly associated with lower water-levels. These conditions reversed during the Last Glacial Maximum (23.0-18.0 cal ka BP) when our data suggest higher runoff and lake productivity and a return to anoxic bottom waters as a result of rising water-levels. Our high-resolution geochemical record reveals the presence of short-term climate stages globally known as Heinrich Stadials (HS), Greenland Interstadials (GI) and Greenland Stadials (GS). The Lake Petén Itzá record indicates that HS and GS were generally dry, while the GI were characterized by higher runoff and wet conditions. Thi variability in runoff correlates with shifts in the average position of the Intertropical Convergence Zone during the Late Pleistocene. The northern Neotropics are strongly affected by current global warming; our data provides important information regarding the potential future behaviour of the northern Neotropics both in long-term and short-term climate change scenarios.