This research assesses the extent to which interacting human and environmental pressures have driven and are driving aquatic ecosystem change in deep freshwater lakes in the warm tropics. Specifically, to assess the extent to which aquatic changes represent an irreversible shift in ecological regime in three deep freshwater lakes (>10 m) in a small part of the Philippines. Regime shifts can force lake ecosystems to an alternate stable state. An alternate stable state (ASS) can be defined as an ecosystem having multiple ASSs for a given combination of parameters and in the event of gradual changes or a sudden perturbation, an ecosystem can be forced to an ASS. Globally, ASSs have been detected in shallow freshwater lakes (<10 m), as a result of feedback processes such as water mixing, sediment resuspension, and macrophyte interaction with water clarity. Because the relative magnitude of these processes decreases with lake depth, it is uncertain whether ASSs exist in deep, thermally stratified lakes. Palaeolimnology is used to test ASS theory for deep lakes that experience similar climatic conditions but different levels of human pressures. Sediment cores were radiometrically dated and analysed for organic matter (OM), spheroidal carbonaceous particles (SCPs), chlorophyll-a (chl-a), elemental geochemistry, pollen, charcoal, and diatoms. Sedimentary evidence was compared with climate and water quality data, in addition to local observations and historical documents. The sediment record estimates environmental change for the past ca. 1000 years and shows a trajectory of increased water pollution and nutrient enrichment from human activity. Climate, land cover change, and eutrophication are interacting drivers of lake response, with the largest contribution being nutrient loading from intensive aquaculture at ca. 1980 CE. Climate warming effects are exacerbated by human drivers, particularly eutrophication from intensive aquaculture. However, not all the requirements for ASS theory are met.