Beach Protection Act of 2008 - (Sec. 2) Amends the Federal Water Pollution Control Act (commonly known as the Clean Water Act) to authorize states or local governments, in carrying out coastal recreation water quality monitoring and notification programs, to develop and implement a coastal recreation waters pollution source identification and tracking program for waters adjacent to beaches or similar points of access that are used by the public and that are not meeting applicable water quality standards for pathogens and pathogen indicators. Requires states or local governments, if they identify a source of pathogenic contamination, to make information on the existence of such source available to the public on the Internet within 24 hours.Authorizes appropriations for grants to states and local governments for developing and implementing monitoring and notification programs for FY2007-FY2012. Prohibits such funds from being used for a congressional earmark.(Sec. 3) Authorizes appropriations to carry out the Beaches Environmental Assessment and Coastal Health Act of 2000 through FY2012.(Sec. 4) Requires a state recipient of a monitoring and notification program grant to report to the Administrator of the Environmental Protection Agency (EPA) on actions taken to notify state environmental agencies with authority to prevent or treat sources of pollution in coastal recreation waters when water quality standards are exceeded.(Sec. 5) Requires grant recipients to identify: (1) the use of a rapid testing method to detect levels of pathogens or pathogen indicators that are harmful to human health; (2) the availability of a geographic information system database that a state or local government program shall use to inform the public about coastal recreation waters; (3) measures for communicating the results of a water sample concerning pollutants within 24 hours of receipt to specified officials and all state agencies with authority to require the prevention or treatment of the sources of pollution in coastal recreation waters; (4) measures for an annual report to the Administrator on the occurrence, nature, location, pollutants involved, and extent of any exceeding of applicable water quality standards for pathogens and pathogen indicators; (5) a publicly accessible and searchable global information system database, with information updated within 24 hours of its availability, organized by beach and with defined standards, sampling plans, monitoring protocols, sampling results, and the number and causes of beach closures and advisory days; (6) measures for the immediate posting of signs at beaches that are sufficient to give public notice following the results of any water quality sample that demonstrates an exceeding of applicable water quality standards for pathogens and pathogen indicators for the adjacent waters; and (7) measures to ensure that closures or advisories are made within 24 hours after a state government determines that its coastal recreation waters are not meeting water quality standards for pathogens and pathogen indicators. Requires the Administrator to: (1) include a revised list of rapid testing methods in the publication of new or revised water quality criteria; (2) publish with such criteria a list of pathogens and pathogen indicators studied; (3) complete an evaluation and validation of a rapid testing method for the water quality criteria and standards for pathogens and pathogen indicators by October 1, 2010; and (4) publish guidance for the use, at coastal recreation waters adjacent to beaches that are used by the public, of rapid testing methods that will enhance the protection of public health and safety through rapid public notification of any exceeding of applicable water quality standards for pathogens and pathogen indicators. Defines the term "rapid testing method" as a method of testing the water quality of coastal recreation waters for which results are available as soon as practicable and not more than six hours after a water quality sample is received by the testing facility.(Sec. 8) Requires: (1) a review by the Administrator of state and local compliance with statutory and regulatory requirements and grant conditions; (2) corrective actions by governments not in compliance; (3) a review by the Comptroller General of such compliance review and corrective actions; and (4) a study and a report by the Administrator on the formula for the distribution of grants for coastal recreation water quality monitoring and notification programs.(Sec. 12) Requires the Administrator to assess and report to Congress on the benefits of using molecular diagnostics for monitoring and assessing the quality of coastal recreation waters adjacent to public beaches.(Sec. 13) Requires the Administrator to: (1) review and update as necessary existing monitoring protocols for mercury affecting the coastal recreation waters of the Great Lakes; and (2) develop updated recommendations on testing for mercury affecting such waters, including in Great Lakes sediment and fish tissue. Authorizes appropriations. (Sec. 14) Requires the Administrator to update the national list of beaches within 12 months after this Act's enactment and biennially thereafter (currently, periodically).(Sec. 15) Requires the Administrator to study and report to Congress on the long-term impact of climate change on pollution of coastal recreation waters.