Algae, the dominant primary producers in many aquatic ecosystems, are critical to global biogeochemical cycling, and changes in their abundance and composition can cascade throughout aquatic food webs. Diatoms often dominate the algal communities in many freshwater systems. Their population dynamics are affected by a variety of environmental variables, many of which are linked to changes in water column properties and habitat availability, which themselves can be linked to shifts in ice cover, length of the growing season, thermal stability and stratification, vertical mixing patterns, habitat alterations, and the availability of resources such as light and nutrients. Climate has strong moderating controls on all of these fundamental aquatic processes, which can directly and indirectly alter species composition, abundance and seasonal dynamics of both periphytic and planktonic diatoms. In this review, we examine the role that climate-mediated alterations in inter-related lake processes have played on diatom community composition, dynamics and size structure, with particular attention to the recent success of planktonic diatom species relative to heavier tychoplanktonic and small benthic diatoms. We focus primarily on paleolimnological records, but also reference a wide spectrum of limnological and physiological studies to review and discuss how climate-driven shifts in lake properties may affect diatom assemblage reorganization. Understanding the limnological and historical context of these often complex diatom changes is key to making scientifically defensible interpretations of paleolimnological records. We further evaluate the plausibility of alternative explanations (e.g. atmospheric nitrogen deposition) for the recent success of small cyclotelloid species by examining trends in these planktonic diatoms from a large number of sites. Using a weight-of-evidence approach, we conclude that recent climate change is the main driver that has led to ecological tipping points resulting in the recent success of small planktonic diatoms that have been reported in many aquatic systems.