Abstract: Lake sediments in the Yellow River reached are important geological carriers that record the overflow, diversion, and sedimentary environment changes of the river. Previously, it was difficult to effectively distinguish the Yellow-River-soured materials from those from other sources in the region, our knowledge of provenance and sedimentation in the lakes in the lower Yellow River reaches were inaccurate, which affected the comprehension of the changes in the lower Yellow River and the evolution of the sedimentary environment. The magnetic mineral characteristics of modern sediments and lake boreholes in the lower reaches of the Yellow River were studied. The sources of floodplain sediments in the Dayeze Lake borehole and the major sedimentary processes recorded in the Huangdun Depression borehole sediments in the northern Jiangsu were analyzed, from which key information of changes in river channel and sedimentary environment of the lower Yellow River reaches was extracted. Based on the differences in magnetic mineral types, particle sizes, and components, the main source of flood sediments in the Dayeze Lake borehole was identified as Yellow River silt, which confirms the effectiveness of magnetic mineral characteristic analysis in source identification and can be used to explore lake sedimentary processes. Furthermore, through the comprehensive analysis of high-resolution environmental magnetic indicators and environmental proxy indicators such as particle size and total organic carbon (TOC), it was revealed that since the early/middle Holocene (～9712 aBP), the sedimentary environment in the Huangdun Depression underwent very different sedimentation processes and the major transition from lacustrine terrigenous clastic facies to river flood facies took place at ～4201 aBP, indicating the earliest time when the Yellow River affected the Huangdun area in the northern Jiangsu. The above provenance analysis based on magnetic mineral characteristics and the discussion on sedimentary environment changes provide important scientific references for a deeper understanding of the changes in the lower reaches of the Yellow River and its relationship with lakes.