Little is known about the distribution and risk levels of nutrients and organic matter (OM) in the surface sediment of shallow submerged macrophyte-dominated lakes. In the current study, sixty surface sediment samples were collected from Xukou Bay, a typical submerged macrophyte-dominated zone in Lake Taihu, China. A 60-day degradation experiment of Potamogeton malaianus, a dominant species in the bay, was done in the laboratory. The results demonstrated that the ranges of total nitrogen (TN) and total phosphorus (TP), alkali-hydrolyzable nitrogen (AN), available phosphorus (AP), and OM in the surface sediment of the bay were 262.2–2,979.6 mg/kg, 41.2–728.7 mg/kg, 8.6–150.0 mg/kg, 4.4–36.4 mg/kg, and 3.7–50.2 g/kg, respectively. The spatial distributions of TN, OM, and AN concentrations showed similar trends: The highest concentrations were present in the northeastern and southwestern zones, while the TP and AP concentrations were high in the northeastern, central, and southwestern zones. The heterogeneity in the spatial distribution of nutrients and OM in the surface sediment of the bay was associated with aquatic vegetation and anthropogenic activities. The comprehensive risk index and organic nitrogen index revealed that the surface sediment was moderately, interactively contaminated by TN and TP and by organic nitrogen. TN and OM in the northeastern zone were mainly derived from endogenous residues due to the decomposition of aquatic plants, while TN in the southwestern zone was primarily derived from agricultural wastewater. Consequently, targeted measures should be implemented to reduce TN and OM in the surface sediment of macrophyte-dominated lakes.