A long-term monitoring program was initiated in 2002 on running and standing waters in a high elevation cirque landscape (Macun) in the Swiss National Park. The region comprises contrasting basins with different water sources, a glacier-fed basin and two precipitation-fed basins. Sampling of 26 permanent and temporary ponds (or small lakes) and of interconnecting streams (IO sites) was conducted from 2002 to 2010. Pond macroinvertebrate assemblages were dominated by chironomids with 42 taxa. The Orthocladiinae were the dominant subfamily in richness and abundance with 22 taxa. The greatest diversity was found in ponds located in the south and outlet basins. The inter-year variability for the same pond is high, but no clear temporal trend was noticed in ponds frequently monitored ponds. The Orthocladiinae subfamily was also the richest in the stream sites where 33 taxa were collected. The north and south basins were separated on the basis of chironomid assemblages. The chironomid assemblages in the stream network shows a temporal trend from 2002 but it cannot be linked to any clear change at the community structure level. The higher richness and abundance in stream sites and ponds of the south basin could be related to a greater heterogeneity in water physicochemistry and substrata, and by the presence of Bryophyta. The understanding of the environmental factors that influence fauna! assemblages is crucial for the protection of this sensitive alpine pond network where a relatively high overall regional diversity (49 taxa) is detected. From the literature, temperature is recognized as the driving force on changes in chironomid assemblages in alpine systems. Our results support the use of chironomids as flagship indicators in the assessment of climatic change in alpine landscapes.