The excessive nutrient loading in lakes and reservoirs poses significant threats to water quality and ecological health, especially under the influence of global climate change and intensified human activities. This study focuses on the long-term trends in nutrient content and ratios, as well as their driving factors in six major lakes and reservoirs (Chaohu Lake, Danjiangkou Reservoir, Dianchi Lake, Dongtinghu Lake, Poyanghu Lake, and Taihu Lake) within the Yangtze River Catchment from 2002 to 2021. Utilizing Redundancy Analysis, Random Forest and Generalized Additive Model, we identify the shifts in natural and socio-economic factors influencing nutrient concentrations and predict future trends under various scenarios. The main driving factors of nutrient content and their ratios have undergone significant changes at different historical stages, with livestock poultry breeding (LPB) and hydraulic retention time (Res_time) being consistently influential. Our findings highlight the dominant role of livestock and poultry breeding and hydraulic retention time in shaping TN content, whereas TP levels are significantly affected by both natural factors (Temperature and Rainfall) and socio-economic activities. Scenario analyses reveal that despite improvements in water management, nutrient loads remain high, posing ongoing risks of eutrophication. Future lakes nutrient content can meet existing water quality standards under socio-economic development scenarios that significantly reduce hydraulic retention time and the contributions of livestock poultry breeding and other socio-economic drivers.