In recent decades, lakes in arid central Asia have undergone severe ecological and environmental changes due to accelerated climate warming and intense human activities. However, there have been few studies that integrate multi-community dynamics, long-term historical trends, and drivers of ecological change, limiting our ability to effectively manage the evolution of these freshwater ecosystems. In this paper, we analyze high-resolution biotic proxies (subfossil cladocerans and diatoms) from Bosten Lake and Ailike Lake, northwest China, over the past two centuries, and compare these records with other lakes in the region to reveal changes in lake ecosystems. Our results indicate that natural climate variability was the primary driver of a first transition (similar to 1910 CE), whereas anthropogenic forcings predominantly drove a second transition (similar to 1960 CE) in these dryland lakes. After similar to 1960 CE, planktonic eutrophic cladoceran species such as Bosmina longirostris and diatom species including Fragilaria cf. crotonensis, Cyclotella atomus, and Cyclotella meneghiniana became more dominant. Redundancy analysis and variance partitioning analysis suggest that changes in community assemblages were mainly driven by nitrogen loading (TN and/or delta N-15), with additional influences related to lake productivity (Chl-a and TOC) and global warming. Furthermore, another shift in cladoceran composition in Bosten Lake, commencing similar to 1990 CE, from large-sized Daphnia to small-sized Bosmina, was likely caused by increased predation pressure as result of the introduction of commercial fish farming. Our findings highlight the importance of understanding the complex interactions of lake ecological shifts with compounded stressors, both climate and anthropogenic forcings, for sustainable water management strategies, enhancing ecological resilience, and protecting freshwater ecosystems from further degradation.