Water Quality and Environmental Innovation Act This bill establishes and transfers funds to the Water Quality and Environmental Innovation Fund. Until September 30, 2028, the Environmental Protection Agency (EPA) may use the fund to award grants and contracts to carry out projects (1) that use emerging technologies (e.g., artificial intelligence or quantum information science) to address threats to water quality; or (2) for the research, development, or design of such technologies. Threats to water quality that may be addressed under a project carried out using a grant or contract may include acidification; the accumulation of plastics, trash, and microplastics; hydrologic alterations, such as restricting tidal flow; nutrient release and eutrophication, including harmful algal blooms; sea-level rise; waste carbon dioxide accumulations; adverse soil health conditions; erosion and sedimentation; and karst, sinkholes, and land subsidence. At the start of each fiscal year from FY2024 through FY2028, an amount of funding must be transferred to the fund that is equal to the amount that the EPA determines will be collected in such fiscal year from fees and charges under the Motor Vehicle and Engine Compliance Program of the EPA.