Algal blooms and sediment diatoms are crucial indicators of lake water ecology, influenced by water quantity and quality. However, the coupled effects of water quality and quantity changes on algal blooms are still unclear, especially for lakes in cold and arid regions. This study assessed the long-term variations in algal blooms in Hulun Lake using a novel approach combining remote sensing and sediment core samples for diatom analysis. Two mutation points from the structural change test were identified in approximately 2000 and 2010 for algal bloom area (MBE) and sediment diatom richness, indicating asynchronous algal blooms. A structural equation model (SEM) demonstrated that water level (WL) changes were the dominant influencing factor, co-driving the variations in algal blooms and sediment diatoms in conjunction with total nitrogen (TN), total phosphorus (TP), and chemical oxygen demand (COD). The results revealed nonlinear relationships between the lake WL, TN, Chla, and COD. The water level of 543 m emerged as a critical threshold affecting the relationship between water quality and quantity. Distinct differences in this relationship were observed when water levels were above or below this threshold. These variations became particularly pronounced during periods of high and low water levels. The results provide novel insights into the dynamics of algal blooms and can further support lake ecosystem conservation and management.