In the recent decades, the area of seasonal water (SEW) has substantially increased at the global scale. To evaluate nutrient dynamics in aquatic ecosystems, previous studies have analyzed the determining factors of sediment nutrient content and stoichiometry on whole sediment profiles without depth separation on SEW sites. Such a methodology assumes that SEW sediment is a uniform unit and its nutrient dynamics are regulated by the same mechanism at various depths (uniformity assumption). We tested this assumption using sediment samples from six depth increments of 154 sediment profiles (1 m depth) on SEW sites at Shengjin Lake in subtropical China. We measured sediment total nitrogen (STN), total phosphorus (STP), nutrient fractions, and the molar ratio of STN to STP (RSNP), and investigated their determining factors at various depths. STN, STP, and RSNP were averaged at 1.34 g/kg, 0.55 g/kg, and 5.43, respectively, and all gradually decreased with depth. STN was positively affected by moisture and flooding duration in all depth increments. Instead, the major determining factors of STP changed from particle size at 0–20 cm of depth to pH and electrical conductivity at 30–100 cm of depth. These vertical patterns have close connections with sediment nutrient fractions since sediment N fractions did not shift along profile depths (i.e., over 99 % of STN was organic N) but sediment P fractions did (the percentage of Fe-P and Al-P decreased by 6.25 % but those of Ca-P increased by 4.31 % along the sediment depth gradient). The major determining factors of RSNP showed no obvious vertical patterns because they frequently varied along depth gradients. The results demonstrate that SEW sediment is not a uniform unit and the determining factors of nutrient dynamics change with depth. Our study highlights the importance of improved methodological reflection in studies addressing sediment nutrient dynamics on SEW sites.