Water Resources Development Act of 2020 This bill addresses water resources infrastructure funding as well as Army Corps of Engineers projects for navigation, flood risk management, and ecosystem restoration. The bill removes from annual discretionary spending limits funds appropriated from the Harbor Maintenance Trust Fund (HMTF) for harbor operations and maintenance purposes, up to a specified amount. This allows additional funds from the HMTF to be appropriated for these purposes without these amounts counting against annual discretionary spending limits. Similarly, the bill removes from annual discretionary spending limits in FY2021-FY2030 funds appropriated for harbor maintenance activities at certain donor ports or energy transfer ports, up to a specified amount. Further, the bill expands the eligible uses of HMTF funds to include maintenance dredging at certain emerging harbors. In addition, the bill modifies cost-sharing requirements for the construction of inland waterway navigation projects. The bill also establishes various pilot programs to address issues including flood risk management and hurricane and storm damage risk reduction in rural or economically disadvantaged communities. Additionally, the bill establishes programs for controlling certain invasive species. The bill also creates a process to deauthorize certain projects that are no longer viable for construction and authorizes new projects for purposes including navigation, flood risk management, and ecosystem restoration.