<p>Sub-lakes (isolated lakes during low water level) of Poyang Lake play critical roles in maintaining biodiversity, regulating water quality, and supporting food webs. Excess nutrient in these sub-lakes caused eutrophication, and was therefore increasingly concerned. However, the underlying mechanisms of nutrient dynamics remain unclear, especially under extreme weather conditions. We selected a typical sub-lake (Zhanbei Lake) of Poyang Lake as the study area. Its phosphorus and nitrogen dynamics during a typical water year (2021) and an extreme drought year (2022) was examined using a process-based model of the environmental fluid dynamics code (EFDC) model. A factor contribution index (FCI) was calculated based on scenario simulations to identify the drivers and their impacts on nutrient dynamics. Results show that extreme drought intensified the impacts of precipitation on total nitrogen (TN) dynamics, with a contribution increasing from 30.8% in typical water year to 74.4% in extreme drought year. For total phosphorus (TP) dynamics, precipitation had a contribution of 18.8% in typical water year, compared with that of 37.3% in extreme drought year. Other drivers affecting TP dynamics included the initial TP conditions of the sub-lake. This study demonstrated the high potential of process-based models in exploring the cause-effect relationships between nutrient dynamics and extreme drought within this unique sub-lake ecosystem.</p>