Global warming affects the hydrological cycle by increasing the frequency and intensity of extreme rainfall events and dry spells. These changes potentially affect the quantity and quality of dissolved organic matter (DOM) input into lakes. In this study, we investigated if changes in precipitation over a 3-year period correspond to changes in DOM and whether these changes affect light attenuation and plankton community composition. We sampled Lake Escondido, a shallow, oligotrophic Andean lake, nine times, analyzing coloured DOM and plankton community composition. During the study period, we observed that variations in the precipitation regime correlated with DOM parameters (water colour and molecular weight), and this, in turn, affected the plankton composition. Chlorophyll a concentrations of both phytoplanktonic fractions (less than and greater than 2 μm) were related to water colour and TDP. We observed in the small fraction ( 2 μm) presented two biomass peaks corresponding to increases of the cyanophyte Chroococcus planctonicus and of the haptophyte Chrysochromulina parva. As precipitation decreased, the lake became more transparent, favouring C. planctonicus and mixotrophic oligotrich ciliates with endosymbiotic Chlorella. In the context of global climate change, our results highlight the potential impact of changes in precipitation patterns and, consequently, in DOM quality on the plankton community.