Water Quality Investment Act of 2009 - Title I: Water Quality Financing - Subtitle A: Technical and Management Assistance - (Sec. 1101) Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act [CWA]) to authorize the Administrator of the Environmental Protection Agency (EPA) to make grants to nonprofit organizations to provide: (1) technical assistance to rural and small municipalities and tribal governments for planning, developing, and financing eligible state water pollution control revolving fund projects; (2) technical assistance and training to enable rural, small, and tribal publicly owned treatment works (POTWs) and decentralized wastewater systems to protect water quality and comply with the CWA; and (3) information to rural, small, and tribal municipalities and municipalities that meet specified affordability criteria with respect to planning, design, construction, and operation of POTWs and decentralized wastewater treatment systems. Authorizes appropriations for FY2010-FY2014 for implementing: (1) such grants; and (2) specified grant programs, training, and EPA programs relating to the causes, prevention, reduction, and elimination of water pollution. Requires the Administrator to make available a specified amount to support an EPA clearinghouse that collects and disseminates information on small flows of sewage and innovative or alternative wastewater treatment processes and techniques. (Sec. 1102) Authorizes appropriations for FY2010-FY2014 for: (1) grants to states for administering programs for the prevention, reduction, and elimination of pollution; (2) watershed pilot projects (currently, wet weather watershed pilot projects); (3) grants to states for water pollution control revolving funds; (4) a pilot program for alternative water source projects; (5) sewer overflow control grants; (6) remediation of sediment contamination in areas of concern in the Great Lakes; and (7) a public information program to provide information relating to the remediation of contaminated sediment in U.S. public areas of concern. (Sec. 1103) Revises provisions relating to watershed pilot project grants. Expands the types of projects eligible for technical assistance and grants to include: (1) efforts of municipalities and property owners to demonstrate cooperative ways to address nonpoint sources of pollution to reduce adverse impacts on water quality; (2) the development of an integrated water resource plan for the coordinated management and protection of surface water, ground water, and stormwater resources on a watershed or subwatershed basis to meet the objectives, goals, and policies of the CWA; and (3) the development of a municipality-wide plan that identifies the most effective placement of stormwater technologies and management approaches to reduce water quality impairments from storm water on a municipality-wide basis. Requires the Administrator to report to Congress on the results of such grants by October 1, 2011. Subtitle B: Construction of Treatment Works - (Sec. 1201) Provides that a community seeking financial assistance from the state water pollution control revolving fund for the replacement or major rehabilitation of a sewage collection system existing on January 1, 2007, or for the construction of a new system shall be eligible for such assistance, provided: (1) the replacement and rehabilitation of the existing collection system or the new collection system is to address an existing adverse environmental condition; and (2) the project otherwise meets the requirements of the CWA. (Sec. 1202) Amends the definition of "treatment works" to include the acquisition of lands and interests in land that are necessary for construction. Subtitle C: State Water Pollution Control Revolving Funds - (Sec. 1302) Revises requirements for capitalization grant agreements with states for establishing water pollution control revolving funds, including by: (1) requiring states to set aside 15% of funds for assistance to municipalities of fewer than 10,000 individuals that meet specified affordability criteria; and (2) applying prevailing wage payment requirements to the construction of treatment works pursuant to a state water pollution control revolving fund or a water pollution prevention and control grant. (Sec. 1303) Expands the types of projects eligible for assistance from such funds to include: (1) the implementation of lake protection programs and projects; (2) repair or replacement of decentralized wastewater treatment systems that treat domestic sewage; (3) measures to manage, reduce, treat, or reuse municipal stormwater, agricultural stormwater, and return flows from irrigated agriculture; (4) measures to reduce the demand for POTW capacity through water conservation, efficiency, or reuse; (5) the development and implementation of watershed pilot projects; and (6) measures to reduce the energy consumption needs for POTWs, including the implementation of energy-efficient or renewable-energy generation technologies. Authorizes states to extend the repayment period for a fund loan from the current limit of 20 years to the lesser of 30 years or the design life of the project to be financed with the proceeds. Conditions eligibility for a loan on the recipient developing and implementing a fiscal sustainability plan for any portion of the treatment works proposed for repair, replacement, or expansion. Sets forth plan elements. Revises the types of assistance that may be provided under state water pollution control revolving loan funds. Authorizes fund grants to owners and operators of treatment works: (1) that serve a population of 10,000 or fewer for technical, planning, and financial management assistance, user fee analysis, budgeting, capital improvement planning, facility operation and maintenance, equipment replacement, repair schedules, and other activities to improve wastewater treatment plant management and operations; and (2) for assessing the energy and water consumption of the treatment works and evaluating potential opportunities for energy and water conservation through facility operation and maintenance, equipment replacement, and projects or activities that promote the efficient use of energy and water. Authorizes states to provide additional subsidization, including forgiveness of principal and negative interest loans, to benefit specified municipalities or to implement a process, material, technique, or technology to address water-efficiency goals, address energy-efficiency goals, mitigate stormwater runoff, or encourage environmentally sensitive project planning, design, and construction. Requires states to: (1) establish affordability criteria to assist in identifying municipalities that would experience a significant hardship raising revenue for fund projects; (2) establish a list of fund projects that prioritizes water quality improvement projects for FY2011 and thereafter; (3) provide financial assistance to only projects on such list; and (4) provide an explanation if they do not fund projects in priority order. Requires the Administrator: (1) by September 30, 2011, to publish a formula for the allotment of fund amounts based on water quality needs in accordance with the most recent survey of needs developed by the Administrator; and (2) to prepare and make publicly available an annual report on the performance of the projects and activities implemented with fund assistance. (Sec. 1307) Requires the Administrator to: (1) assist states in establishing simplified procedures for treatment works to obtain assistance; and (2) publish a manual to assist treatment works in obtaining assistance. Prohibits state water pollution control revolving funds from being used for the construction of treatment works unless the steel, iron, and manufactured goods used in such treatment works are produced in the United States. (Sec. 1308) Authorizes appropriations for capitalization grants for state water pollution control revolving funds for FY2010-FY2014. Prohibits any of such funds from being used for a congressional earmark. Subtitle D: General Provisions - (Sec. 1402) Requires the Administrator to reserve a specified amount of state water pollution control revolving funds for Indian tribes for FY2009 and thereafter. Requires such reserved funds to be used to serve: (1) Indian tribes; (2) former Indian reservations in Oklahoma; and (3) Alaska Native villages. Subtitle E: Tonnage Duties - (Sec. 1501) Increases the tonnage duty (currently, a tax) on specified vessels entering or returning to a U.S. port for FY2010-FY2019. (Sec. 1502) Requires the Administrator to: (1) study and report to Congress on wastewater treatment facilities that discharge into the Rio Grande River; and (2) develop recommendations for improving monitoring, information sharing, and cooperation between the United States and Mexico. Requires the Comptroller General to: (1) study and report to Congress on water infrastructure along the border between the United States and Mexico to augment current studies relating to colonias development; and (2) examine the comprehensive planning needs relating to water and wastewater infrastructure for colonias along such border. Title II: Alternative Water Source Projects - (Sec. 2001) Requires the Administrator, in making grants for the pilot program for alternative water source projects, to consider whether a project is located in an area which is served by a public water system serving 10,000 individuals or fewer. Authorizes appropriations for such grants for FY2010-FY2014. Tittle III: Sewer Overflow Control Grants - (Sec. 3001) Requires the Administrator to: (1) ensure that a state uses at least 20% of its sewer overflow control grants to implement projects to control municipal combined sewer overflows and sanitary sewer overflows through the use of green infrastructure, water and energy efficiency improvements, and other environmentally innovative activities; and (2) report to Congress by December 31, 2012, and periodically thereafter on recommended funding levels for sewer overflow control grants. Authorizes appropriations for such grants for FY2010-FY2014. Title IV: Monitoring, Reporting, and Public Notification of Sewer Overflows - (Sec. 4001) Amends the National Pollutant Discharge Elimination System to direct the Administrator or a state to require the owner or operator of a POTW to monitor, provide notification to the public, public health authorities, and other affected entities of, and report on, sewer overflows. Provides for the approval of state notification programs. Title V: Great Lakes Legacy Reauthorization - (Sec. 5003) Amends the Great Lakes Legacy Act of 2002 to authorize appropriations for FY2010-FY2014 for research on the development and use of innovative approaches, technologies, and techniques for the remediation of sediment contamination in U.S. areas of concern. (Sec. 5004) Requires the Administrator to: (1) study and report to Congress on the condition of wastewater treatment facilities located in the United States and Canada that discharge into the Great Lakes; (2) determine the effect that such facilities have on the water quality of the Great Lakes; and (3) develop recommendations to improve water quality monitoring by the operators of such facilities, establish a protocol for improved notification and information sharing between the countries, and promote cooperation between the countries to prevent the discharge of untreated and undertreated wastewater. Title VI: Pharmaceuticals and Personal Care Products - (Sec. 6001) Requires the Administrator to: (1) study and report to Congress on the presence of pharmaceuticals and personal care products (PPCPs) in U.S. waters; and (2) identify PPCPs that have been detected, the levels of detection, the sources of PPCPs, and methods to control, limit, treat, or prevent PPCPs. Title VII: Miscellaneous - (Sec. 7001) Requires the Administrator to convene a task force to develop and report to Congress on: (1) recommendations on the proper disposal of unused pharmaceuticals by consumers, health care providers, and others; and (2) a strategy for the federal government to educate the public on such recommendations. Terminates the task force 180 days after the submission of such report. Title VIII: OMB Study - (Sec. 8001) Requires the Director of the Office of Management and Budget (OMB) to evaluate and report to Congress on the programs authorized by this Act under the Program Assessment Rating Tool or a successor performance assessment tool. Title IX: Chesapeake Bay Accountability and Recovery - (Sec. 9001) Requires the Director to report annually to Congress on: (1) a Chesapeake Bay interagency crosscut budget; (2) an accounting of all funding amounts of at least $100,000 received and obligated by federal agencies for restoration activities that protect, conserve, or restore water quality in the Chesapeake Bay watershed; (3) an accounting from each state of all funding amounts of at least $50,000 received and obligated from a federal agency for restoration activities; and (4) a description of each of the proposed federal and state restoration activities. (Sec. 9002) Requires the Administrator to: (1) implement an adaptive management plan for restoration activities and update it every three years; and (2) report to Congress annually on such plan.