The impact of global warming on lake ecosystems has been of central and growing interests to limnologists recently. Here, we describe the strengths and weaknesses of the multi-faceted approaches that are presently available for elucidating the effects of climate change on phytoplankton, including time series, space-for-time substitution, remote sensing, experiments, modeling and palaeolimnology. Phenology has been impacted due to rising temperatures, earlier thermal stratification and the disappearance of ice-covers on some lakes. These changes have greatly favored increasing dominance by cyanobacteria in lakes globally. Species-specific changes have been observed in response to global warming in different regions around the globe. In lakes where nutrient supplies are sufficient, primary production of phytoplankton has been enhanced by global warming. However, primary production might be more inhibited when nutrients are limiting. Because environmental factors invariably interact with each other, knowing how to evaluate the effects of a single factor on phytoplankton composition and activity is the key research challenge. Changes in wind speed and patterns caused by global warming may affect nutrient releasing, as well as the light regimes in the water column in shallow lakes. Therefore studies on wind-driven effects of sediment and nutrient resuspension events induced by global warming on phytoplankton community succession in large shallow lakes are a future research frontier in limnology.