Though mountain lakes are generally much less influenced by human activities than other habitats, global and local anthropogenic threats can alter their natural condition. The most alarming threats are climate change, water exploitation and abstraction, alien species introduction, and the medium-long range atmospheric transport of contaminates. Moreover, tourism and mountain farming are two other major sources of organic pollutants that can pose a threat to local aquatic biodiversity. Papers submitted to this Special Issue should be original contributions, with a focus on ecological and morphological characterization, environmental pressures (i.e., alien species introduction, environmental contaminates), and the use of bioindicators/tracers to inform adequate management plans.