Abstract Global environmental change is threatening freshwater biodiversity with ecological impacts predicted to be particularly severe in high‐altitude regions. Despite this, an ecological understanding of high‐altitude pond networks remains patchy, with only limited knowledge of the environmental and spatial predictors of taxonomic and functional diversity. Moreover, previous studies of pond ecosystems have focused primarily on taxonomic richness and largely overlooked functional diversity. This study examined the influence of local environmental and spatial factors on taxonomic and functional α and β diversity (including the turnover and nestedness‐resultant components) of 17 high‐altitude (~2,500 m above sea level) pond macroinvertebrate communities, in the Macun Cirque, Switzerland. Spatial processes (pond connectivity) were important drivers for taxonomic α diversity, while local environmental variables (pond permanence and surface area) were important determinants of functional α diversity. Species turnover was the most important component of β diversity for taxonomic composition, and functional composition demonstrated a nested spatial pattern. Variation in taxonomic and functional composition (and the turnover and nestedness components of β diversity) were determined by local environmental variables despite the limited environmental gradients within the pond network. No significant effects of spatial variables on community composition were recorded for either facet of diversity, indicating that compositional variation was determined at a local scale. Water temperature, depth and pond permanence were consistently the most important measured drivers of diversity. Given the importance of both spatial and environmental variables in structuring taxonomic and functional diversity, landscape‐scale conservation and management activities that aim to improve or protect high‐altitude freshwater biodiversity should focus on maintaining connectivity among ponds and environmental heterogeneity, particularly pond surface area, water depth, and hydroperiod. Understanding the mechanisms driving taxonomic and functional diversity will be critically important for the management and conservation of macroinvertebrate communities in high‐altitude pond networks in the face of climatic warming.