Microplastic (MP) pollution has garnered global attention in recent years. Although anthropogenic factors have been extensively studied for their impacts on MP pollution, there is still a lack of research on the relationship between non-anthropogenic factors and MP occurrence in inland freshwater. This study investigated MP pollution in Donghu Lake, the largest urban freshwater lake in China, to examine the effects of rainfall and lakeshore soil properties on MP pollution. The MP abundance in the surface water of Donghu Lake was 5.84 ± 2.95 items per L under the equilibrium state. However, during and after rainfall, the MP abundances significantly increased to 8.27 ± 5.65 items per L and 7.60 ± 4.04 items per L, respectively (p < 0.05). This increase could be attributed to an increase in the amount of MPs transported to the lake via atmospheric deposition and rainfall runoff, as well as the re-suspension of MP debris in sediment during stronger hydrodynamics. A statistically significant negative correlation was observed between MP abundance and lakeshore soil particle size. It suggested that a high proportion of large-sized soil particles created large pores that enabled MPs to be deposited in the surface layer of soil to migrate to deeper layers. As a result, the amount of MPs in the surface soil and transported to the lake via surface runoff was low. It is of practical significance to understand the sources and distribution impact factors of MPs in urban lakes. The fate and effects of MPs retained in the inland freshwater environments should receive more attention.