This paper summarizes the initial results from the long-term monitoring program of running and standing waters in a high elevation cirque landscape (Macun Lakes) in the Swiss National Park. The region comprises two contrasting basins with different water sources, a glacier-fed basin and a precipitation-fed basin. Monitoring encompasses annual measures of physico-chemistry of the waters along with samples of macroinvertebrates in midsummer. Monitoring was initiated in 2001 when the area was annexed to the park. Preliminary results indicate the high sensitivity of alpine waters and biota to changes in climate. Results from the stream measures suggest a shift in physico-chemistry (warmer waters, decreases in nitrogen constituents) and zoobenthos (taxa and density decreases) over time that reflected the differences and changes in water source in each basin. Results from the pond monitoring showed the rapid response of these small water bodies to alterations in air temperature and pluviometry. The pond data also demonstrated a strong spatial heterogeneity between ponds in both physico-chemistry and macroinvertebrate composition. The monitoring of both streams and ponds provides a holistic picture of abiotic and biotic changes of alpine waters to landscape and climate change.