Sediment nutrients can be released to the surface water when hydraulic disturbance becomes strong in shallow lakes, which contributes to nutrient enrichment and subsequent lake eutrophication in the water column. To explore the seasonal variations and spatial distributions exhibited by nutrients in the water column, surface sediment, and pore water of Lake Yangcheng and its major tributaries, we determined the concentrations of nitrogen (N) and phosphorus (P) throughout the lake in different seasons of 2018. Total N (TN) and total P (TP) concentrations in the connected rivers were much greater than those in the lake, indicating that external loading greatly contributed to the nutrient enrichment. TN concentration in the water column was highest in the winter, whereas TP peaked in the summer. A similar temporal pattern was observed for TN and TP in the sediment with maxima in the winter and minima in the summer; however, nutrients in the pore water were highest in the summer, in contrast to the temporal variation in the sediment. Additionally, high TN values in the water column and high TP in the three compartments were distributed primarily in the west part of the lake, while high TN concentrations in the sediment and pore water were observed mainly in the east portion of the lake. According to the enrichment factor index (an indicator evaluating the nutrient enrichment by comparing the detected contents and standard values), nutrients in the lake sediment were severely enriched with TN and TP averaging 2195.8 mg/kg and 543.0 mg/kg, respectively. The vertical distribution of TN and TP generally exhibited similar decreasing patterns with an increase in sediment depth, suggesting mineralization of TN and TP by microbes and benthic organisms. More attention and research are needed to understand the seasonality of nutrient exchange across the sediment–water interface, especially in eutrophic lakes.