Submerged macrophyte restoration is the key stage in the reestablishment of an aquatic ecosystem. Previous studies have paid considerable attention to the effect of multiple environmental factors on submerged macrophytes. Meanwhile, few studies have been conducted regarding the spatial and seasonal characteristics of water and sediment properties and their long-term relationship with submerged macrophytes after the implementation of the submerged macrophytes restoration project. On a monthly basis, we monitored the spatial and seasonal variation in water parameters, sediment properties, and the submerged macrophyte characteristics of West Lake in Hangzhou from August 2013 to July 2019. From these measurements, we characterized the relationship between environmental factors and submerged macrophytes. Water nutrient concentrations continuously decreased with time, and the accumulation of sediment nutrients was accelerated as the submerged macrophyte communities developed on a long-term scale. The results indicated that the difference in water parameters was due to seasonal changes and land-use types in the watershed. The differences in the sediment properties were mainly attributed to seasonal changes and changes in the flow field. Redundancy analysis showed that the influence of water nutrients on the submerged macrophyte distribution was greater than that of sediment nutrients. The result also suggested that the developed root system, high stoichiometric homeostasis coefficients of P, and compensation ability of substantial leaf tissue may lead to a large distribution of Vallisneria natans in West Lake in Hangzhou. The correlation of water parameters and sediment properties with submerged macrophytes for a long time was very important as the restoration was achieved. To ensure the stability of the aquatic ecosystem after performing the submerged macrophyte restoration, a greater emphasis must be placed on reestablishing the entire ecosystem, including the restoration of aquatic animals and fish stocks. We expect these findings to serve as a reference for researchers and government agencies in the field of aquatic ecosystem restoration.