Sedimentation is recognized as a major factor determining the ecosystem processes of lake beaches; however, the underlying mechanisms, especially in freshwater sand dunes, have been insufficiently studied. To this end, nine belt transects from nine freshwater sand dunes, classified into low (<23.7 m), medium (25.4–26.0 m), and high-elevation groups (>28.1 m) based on their elevations in 1972, were sampled to investigate differences in sedimentation rate and soil and vegetation characteristics in Southern Dongting Lake, China. Sedimentation rate, soil sand content, and soil pH increased, whereas soil clay, fine silt, moisture (MC), organic matter (OM), total N, and total K content, in addition to the growth and biodiversity of sand dune plants generally decreased with decreasing belt transect elevation. Regression analyses revealed that the negative effects of sedimentation on the ecosystem functions of sand dunes could be attributed to higher fine sand content in deposited sediments and stronger inhibition of plant growth. These results are consistent with previous studies performed in coastal sand dunes, which highlights the importance of sedimentation in determining ecological processes.