Past environmental changes in mountain lakes can be reconstructed with the use of subfossil diatoms from post-glacial sediments. This study applied such an analysis to two mountain lakes in the Sudetes Mts. in Poland: Mały Staw (MS) and Wielki Staw (WS). Cores 882 cm long (MS) and 1100 cm long (WS) taken from the centre of each lake in 1982 were used to study the long-term acidification history of these lakes. Changes in vegetation indicate that the initial phase of MS started at the end of the Pleistocene. WS sediments began to accumulate shortly after that, at the beginning of the Holocene. The majority of the diatom assemblages are typical of oligotrophic acidic lakes located in alpine and arctic regions. A pH reconstruction based on diatoms (DI-pH) showed long-term acidification dating to almost the beginning of the lakes’ existence. Natural acidification began after the deglaciation, and the most intensive acidification continued to the end of the mid-Holocene. Through the whole period studied, pH decreased by 1.4 in MS and 0.9 in WS. After a period of relatively stable lake water pH, it decreased rapidly during the last few decades of the 20th century, due to anthropogenic pollution: pH declined by 0.7 in MS and 0.3 in WS. Mały Staw, being shallower, smaller, and with a larger drainage basin than Wielki Staw, is more sensitive to acid deposition; this accounts for the difference in pH.