Testate amoebae that inhabit peat are sensitive indicators of water table position. In this study, we used testate amoebae in sediments from a mire in the western Alps (Lac du Thyl) to: (1) reconstruct the hydrology of the site over the last 7,000 years, (2) determine how hydrological changes affected testate amoebae diversity and (3) infer past trophic state shifts. The study site is located in one of the driest valleys of the Alps and is thus very sensitive to hydrological changes. Our study revealed that the water table depth increased (dry conditions) between 5,800 and 4,000 cal year BP. This triggered establishment of a Sphagnum-type peat and acidic conditions from 5,700 to 4,000 cal year BP. These processes were independent of ongoing transformations of the terrestrial vegetation and soil in the catchment area. After 1,690 cal year BP, the depth to the water table decreased (wetter conditions) and a minerotrophic fen developed. At the same time, the diversity of testate amoebae increased, probably as a result of deforestation that supported the expansion of grassland. Climate and land use were apparently more important factors controlling the lake hydrology than were changes in vegetation and soil in the catchment. Testate amoebae diversity was linked to land cover. Changes in pH were controlled indirectly by external forcing (climate), but more directly by fluctuations in the level of the water table (internal forcing) and autogenous expansion of Sphagnum.