Climate change has been studied for many decades. Growing scientific, political, and public attention has focused on climate change and its effect on ecosystems, including lake ecosystems. In this study, we conducted comparative quantitative and qualitative analyses that focused on research development, current hotspots, and potential future directions of climate change research associated with lakes using a bibliometric analysis based on the Science Citation Index (SCI) database. A total of 10,296 papers associated with climate change-lake research were published in 1266 journals. Rapid development occurred over the past 25 years and the number of published papers considerably increased since the 2000s. A keyword analysis showed that among the top 50 most frequently used keywords, paleoecology, palynology, paleolimnology, climate change, and pollen analysis exhibited decreasing trends. Recently, eutrophication exhibited one of the highest co-occurrence frequencies with climate change. Keywords such as algae and cyanobacteria also showed increasing trends with climate change, implied that more attention was paid to the harmful cyanobacterial blooms. Another significant increasing trend was observed between climate change and remote sensing, which is a modern technology that is now widely used in limnology. Our results also indicate that a distinct turning point associated with climate change-lake research occurred between 1991 and 2015. Before the 2000s, most studies focused on paleolimnology. Specifically, researchers were searching for the evidence of climate change in lake sediments by using traditional technologies, such as reflecting ancient climate using the information recorded by diatom or pollen in the sediments. Recently, more studies have focused on modern limnology, e.g., the effects of climate change on lake ecosystems. In addition, future research may focus on the following topics: i) the interactive effects of climate change and eutrophication, or other environmental variables, on lake ecosystems; ii) solutions for mitigating the negative effects of climate change; and iii) the potential effects of eutrophication on climate change.