The Pyrenees hold a lake district with a few more than one thousand mountain lakes (> 0.5 ha), about a half of them in each the northern and southern slopes. The lithology varies along the range, and the lakes lie on bedrocks as diverse as granites, slates, schists, limestones, and volcanic materials. The Pyrenees are located in a climatic transition area: the western lakes are more influenced by the Atlantic climate regime, whereas the eastern lakes receive higher Mediterranean influence. And, of course, the lakes are distributed along an altitudinal gradient, spanning from 1600 to nearly 3000 m a.s.l. All these features have an effect on the physics, chemistry and biology of the lakes. Several surveys, carried since 1987 at decadal intervals, have provided a synoptic view of the lake ecosystems of the Pyrenees and revealed the recent temporal trends caused by the diverse environmental drivers at a regional scale.