Water-level fluctuations (WLF) in lakes and rivers, especially their extent, frequency and duration, are dominant forces controlling the functioning of these ecosystems. In particular, WLF play an important role in the lake's littoral and aquatic-terrestrial interface processes. WLF may take place on different spatial and temporal scales under natural conditions but water levels have been artificially modified in regulated lakes, and their impacts are expected to be enhanced within the actual global change scenarios with forthcoming management problems. This article presents an overview on the literature published on this important topic since 1991 by using journals indexed in the ISI Web of Knowledge. The overall objective was to examine temporal and spatial trends in publications on WLF, the specific aspect of WLF concerned and their main effects. Throughout the article we have used case studies to illustrate different effects of WLF on the variety of lake habitats and indicators that have been studied. Overall, the number of papers published on the subject since the 1990s has risen steadily, when less than ten papers were published each year; until 2006 and peaking in 2005. The greatest number of papers on WLF has been carried out in Europe and North America (c. 73%). These data also showed that the effects of WLF have not been studied equally for different groups of organisms. There is a greater interest on macrophytes, which are the most studied group of organisms (18.4% of the papers). Nearly 7% of the papers deal with algae, and zooplankton and invertebrates account for a 7% followed by fish. WLF effects on ecosystems are very complex, and the biological effects in lakes are greatest in shallow water and littoral areas, where even small changes in water levels can result in the conversion of large areas of a standing-water environment in air exposed habitats. Finally, these data might serve to highlight knowledge gaps still existing on this topic and, in particular, some of the approaches that can potentially contribute to solve several of these lacunae are explored.