Lakes located above treeline or alpine ones offer valuable opportunities to assess the effects of natural and human-induced influences, ranging from local to global scales. Further, there is a growing concern about several local threats jeopardizing the ecological integrity of these ecosystems. Zooplankton communities, which essentially comprise the entire pelagic consumer compartment in naturally fishless alpine lakes, can indicate ecosystem changes. Here, we analysed 643 zooplankton samples from 101 lakes and ponds in the Western Alps, collected over 19 years (2006–2024). Community data -taxa and functional groups- were examined to evaluate zooplankton responses to local natural and anthropogenic factors and to detect long-term changes linked to broader regional or global trends. Long-term trends showed declines in cold stenothermal taxa and groups, which are consistent with the effects of climate warming. Despite most lakes being located within protected areas, about half were affected by local anthropogenic factors such as fish introduction and hydroelectric exploitation. Our findings highlight that a critical component of aquatic ecosystems underwent significant taxonomic and functional composition shifts over time, likely due to a combination of climate change and widespread fish introductions. The study emphasises the need for conservation measures and actions to safeguard still pristine alpine lakes and recover impacted ones to enhance mountain aquatic biota resilience to projected global changes.