The transport of sediment particulates and particulate phosphorus (PP) in shallow lakes is critical for sediment accumulation and water quality evolution. To address the unclear mechanisms governing particulate and PP transport in Lake Taihu and their contribution to sediment deposition, this study examined the overall mass balance, transport characteristics, and deposition patterns of suspended solids (SS) and particulate phosphorus entering and leaving the lake. The investigation combined 2024 monitoring of inflow and outflow rivers with a one-month whole-lake sampling campaign in October 2020 that included particle size fractionation, supported by flux balance analysis. Results show that sediment accumulation and associated phosphorus retention in Lake Taihu were pronounced. In 2021, the net SS inflow into the lake was approximately 400000 tons, equivalent to a sediment volume of about 550000 m3 and an annual deposition rate of 0.35 millimeters. During the same period, net PP retention reached 989 tons, with around 73% of the incoming PP entering the lake adsorbed to particulates, indicating that particulate sedimentation serves as the dominant pathway for phosphorus accumulation. Marked differences were observed in particle size distribution and phosphorus speciation between inflow and outflow. Inflowing particulates were dominated by the 20–50 μm fraction, whereas outflowing particulates were primarily in the 0.45–10 μm range. Moreover, the 10–20 μm fraction carried over 80% of the PP. Hydrodynamic processes significantly influenced the spatial distribution of particulates and PP, resulting in a “high in the west and low in the east” pattern for particulates and a “high in the northwest and low in the southeast” distribution for particulate phosphorus.