Eutrophication and harmful algal blooms (HABs) in freshwater lakes and reservoirs are severe global problems for aquatic ecosystems. In particular, severe HABs accumulation in the littoral zone is likely to cause hypoxia (black and odorous water), and thus threaten drinking water safety. Therefore, assessing the risks of HABs accumulation and accurately identifying the littoral zones that is prone to HABs accumulation are of particular importance for water management practice. This study took Lake Chaohu, a large shallow eutrophic lake in the middle and lower reaches of the Yangtze River in China as the study area. Based on the technological advances in hydrological and hydrodynamic modelling in the lake-watershed system, remote sensing monitoring, spatial analysis in GIS software, etc., we developed a novel risk assessment index for HABs accumulation by considering the factors of phytoplankton biomass, shoreline shape, hydrodynamic and wind conditions. The index was applied in Lake Chaohu to assess its risk of HABs accumulation during 2018-2019. The assessment results were divided into five levels from I to V, and were mapped to identify the area with a high risk of HABs accumulation. Our investigation results showed that the high-risk areas of HABs accumulation are mainly located in the western and northwest areas of Western Lake Chaohu, accounting for 12.1% of the littoral zone in Lake Chaohu. These areas should be highly concerned in the emergency management of HABs in Lake Chaohu. The assessment results were generally consistent with our survey findings. The developed risk index for HABs accumulation can be easily transferred to other large eutrophic lakes and reservoirs, and can well support the emergency management practice of HABs.