Enriched sediment can release nutrients to water and is not conducive to the ecological restoration of submerged macrophytes. Sediment capping with zeolite and shale ceramsite (ZSC) before Vallisneria natans (L.) (V. natans) planting was set to research the water quality and characteristics of plant and microbial communities of sediment. The results showed that covering ZSC with V. natans could effectively maintain the low content of total phosphorous (TP) (0.02~0.06 mg/L), total nitrogen (TN) (0.23~1.62 mg/L), ammonia (NH3-N) (0.14~0.63 mg/L), chemical oxygen demand (COD) (6.15~74.83 mg/L), and chlorophyll a (Chl.a) (0.04~0.56 mg/L) in overlying water. Covering ZSC can effectively alleviate the environmental stress of sediment on V. natans in the performance of biomass, height, and chlorophyll of V. natans increasing, the content of ascorbic acid (AsaA), malondialdehyde (MDA), and protein in V. natans decreasing. Covering ZSC creates anaerobic conditions in the sediment, increasing the relative abundance of Levilinea and Longilinea, which may promote the waste anaerobic digestion of sediment. These results, which covered ZSC with V. natans, benefit ecological remediation. It is helpful to offer managers useful information on selecting ZSC and submerged macrophytes for ecological restoration.