Located in the arid semi-arid transition zone at the edge of the East Asian monsoon, the Huangqihai Lake is a typical lake ecosystem that is highly sensitive to climate change and human activities. Clarifying the differences between climate-driven natural evolutionary processes and human-induced ecological changes is a key scientific issue for understanding the response mechanisms of lake ecosystems in this region. In this study, the historical evolution of phytoplankton primary productivity and lake trophic state over the past ~1600 years was inferred in the Huangqihai Lake based on visible reflectance spectroscopy (VRS)-reconstructed chlorophyll a (Chl.a) concentration in sediments and visible-near-infrared spectroscopy (VNIR)-reconstructed total organic carbon (TOC) concentration in lake water. Combined with multi-environmental proxies such as TOC, total nitrogen (TN), total phosphorus (TP), particle size, magnetic susceptibility and geochemical elements in sediments, the evolution of the Huangqihai Lake ecosystem and its main drivers were systematically explored. The results show that before ~820 AD, despite the warm and humid climate and the enhanced East Asian summer monsoon, the runoff from the watershed led to a decrease in the light penetration of lake water, which suppressed the primary productivity of the lake. Between 820 and 1500 AD, the warm and humid climate promoted the vegetation development in the watershed, leading to increased nutrient input into the lake. This nutrient enrichment likely exceeded ecological thresholds, significantly enhancing phytoplankton productivity and TOC concentrations in the lake water. These changes contributed to pronounced shifts in lake ecosystem structure. Since 1500 AD, despite a shift to a cooler and drier climate, intensified agricultural activities in the watershed led to increased soil erosion and nutrient input, maintaining relatively stable algal productivity. In the 20th century, a combination of climate warming, enhanced evaporation, and increased anthropogenic disturbances such as over-exploitation of groundwater and exploitation of lake resources, resulted in a marked decline in lake water levels and algal productivity, indicating a trend of ecosystem degradation. This study reveals the nonlinear and phased evolution of the Huangqihai Lake ecosystem under the combined effects of climate change and human activities, highlighting the profound impacts of land use, groundwater regulation, and hydrological processes on the stability of lake systems in arid and semi-arid regions. These findings provide a scientific basis for ecosystem restoration and adaptive management of water resources in these regions.