Despite covering a small portion of the earth's surface, lakes and reservoirs offer enormous benefits to human society, environmental well-being, and economic welfare. Previous studies have provided insights into specific subjects, yet integrated perspectives on the development of the two waterbodies are missing. To this end, we conducted a bibliometric analysis as a systematic data gathering to perform a large-scale overview and assess global trends of their scientific publications. Moreover, a second goal is to differentiate their research hotspots and current challenges given the different nature of their origin and functionality. 147,811 publications from 1955 to 2019 were retrieved from the database of the Science Citation Index Expanded, and then, divided into four research lines, (1) design and operation; (2) environment and ecology; (3) sanitation and human health; (4) socioeconomics. Bibliometric indicators showed that the number of publications sustained a rapid growth, from 100 during the 1950s to around 7800 publications per year during the past few years. The United States and EU 28 have long been world leaders in lake and reservoir research yet China has tremendously boosted its publications within the past 20 years, advancing this nation to the new world leader in both categories in 2019. Taking a closer look at research hotspots, design and operation have been the main topics for reservoir research while environment and ecology topics are the hotspots in lakes-related studies. This reflected the intensive human interventions in reservoirs, whose major purposes are to supply hydropower energy, irrigation, water storage, and aquaculture. Conversely, the impacts of eutrophication, heavy metals, and climate change have become more severe with the increase of species extinction and biodiversity loss, leading to urgent needs for lake restoration. Both freshwater bodies show comparable attention on their roles in socioeconomics while much higher concerns about sanitation and human health have been paid in reservoirs compared to its counterpart. Clear obtained distinctions in the hotspots and challenges of lake and reservoir research can contribute to better decision support systems of the two waterbodies.