Biodiversity and ecological stability are closely linked, and over recent timescales, anthropogenic impacts have accelerated losses in both from local to global scales. We attempt to show the combined response of diversity and stability of an aquatic community to changes in human activity as a driver. To address this, we measured the diversity and variability of chironomids and their drivers and nature of response to external conditions over the last century, based on 4 lake sediment sequences from Southwest China, one of world's 36 biodiversity hotspots. Our results showed that the driver-response relationship was linear in a lake without direct human impacts but nonlinear in human directly impacted lakes. Recent decreases in alpha diversity and increases in beta diversity were commonly recorded in all four lakes, suggesting that both species loss and a faster replacement of chironomid taxa are a regional phenomenon. However, in the same context of human-induced global warming, increased variability and regime shifts only occurred in lowland lakes, directly disturbed by humans, highlighting that direct human impacts have overcome natural forcing as the determinant driver shaping the chironomid composition in these sites. In addition, we found that increases in beta diversity occurred prior to a regime shift and its character depends on how the community responds to the key external pressure. Our findings reveal that direct human disturbances have largely reshaped the chironomid composition and induced an earlier regime shift at the cost of species loss, resilience loss, and a change in driver-response type.