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Regime shifts in ecology are characterised by major, often abrupt changes in ecosystem structure and functioning in response to one or more driving variables, or pressures. Changes in the provision of ecosystem services are a potential outcome. Despite the current combination of rapidly increasing pressures on what are often highly important socio-ecological systems, the resilience of lakes in the warm tropics to human perturbation is far less well understood than those at higher latitudes. This paper focuses on evidence of aquatic ecosystem change from a cluster of three deep, freshwater, volcanic crater lakes (Yambo, Mohicap, and Sampaloc) at low altitude on the island of Luzon, Philippines. The lakes support different intensities of aquaculture, an important livelihood but also a driver of poor water quality throughout tropical Asia. Measured and monitored climate and water quality data, in addition to sedimentary evidence from sediment cores collected from the three study lakes, were used to determine the magnitude and trajectory of changes in lake water quality. Sediment cores were radiometrically dated and analysed for organic matter, spheroidal carbonaceous particles, and diatom remains. Diatom data were zoned numerically using cluster analysis. Diatom remains were also used to infer past variations in pH and possible relationships between potential driving climatic variables (temperature and rainfall). Diatom data sets were explored using detrended component analysis and principle component analysis. Despite differences in intensity of aquaculture, a common trajectory and timing of a potential regime shift, characterised by a replacement of benthic with planktonic diatoms and an increase in diatom accumulation rates from the early to mid-1980s, is evident, and attests a low threshold for disturbance effects. A predominantly planktonic diatom flora has persisted even after recent improvements in environmental quality. The potential new regime may be less resilient and more susceptible to harmful algal blooms, abrupt expansions of anoxic conditions, and periodic mass fish kills when compared with its former state. The research further highlights the sensitivity of freshwater ecosystems in the warm tropics to disturbance pressures, and the risks to livelihoods, ecosystem services, and sustainable development.