Lakes are important freshwater ecosystems contributing a variety of ecosystem services to the global community, including resource provision, regulatory services, cultural, educational, and religious functions, and ecological supporting services. Lakes' life span and well-being are subjected to anthropogenic activities and climate changes whereby the impacts are related to their variable sizes, depths, morphology, and residence time. Tropical lakes, which are mainly located in areas with high human footprints, face serious challenges primarily due to human-induced and atmospheric influences that quickly degrade their overall health. This chapter discusses the main threats and issues facing tropical lakes and their related impacts, such as eutrophication and toxic algal blooms, sedimentation, the introduction and proliferation of non-native and invasive species, climate change, emerging micropollutant contaminants, water withdrawal, shoreline modification, and acidification. To ensure the sustainability of lakes, good lake governance necessitates a concentrated effort to give priority to the mitigation of negative anthropogenic impacts in lake basins, prevention of invasive species, and efficient management of nutrients, organic matter, and other pollutant inputs into lakes.