With the increasing impact of drought and anthropogenic c activities, middle and high latitude lakes are increasingly facing exacerbated eutrophication. The sister lakes Hulun Lake and Buir Lake, the former located in the Hulunbuir Grassland in northeast China and the latter shared by China and Mongolia, have been exposed to outbreaks of harmful algal blooms (HABs) of varying degrees. In this study, multi-source remote sensing technologies were utilized to explore the essential factors causing HAB occurrences in the Hulun Basin. First, a simplified adjusted floating algae index (AFAI) algorithm was applied to invert the HAB sequence from 1984 to 2019. The results show that large-scale HABs were detected in both lakes on or close to the same days in 1984, 1999, and 2013. From a long-term perspective, the HAB events of Hulun Lake are more serious and intractable than those of Buir Lake in terms of outbreak frequency, duration, and scale. Furthermore, the effects of meteorological and hydrological conditions were evaluated quantitatively. In situ sampling of the two lakes highlights the limiting effect of nutrients on the algae flooding in Buir Lake with perennial outflow. In contrast, Hulun Lake turned into an internal flow lake without outlets from 2000 to 2012 and the decreasing water volume stimulated the accumulation of total nitrogen (TN) and phosphorus (TP), with averages of 2.36 and 0.21 mg/L, respectively. Analysis of the comprehensive driving factors demonstrates that the level of exogenous nutrients caused a difference in the severity of the HAB event between the sister lakes, which are largely determined by drought and eco-unfriendly anthropogenic activities. Our work emphasizes the pivotal role of substantial increases of nutrient loads and stricter regulations are necessary to curb further deterioration of this situation.