Report 2012-120 Summary - June 2013

State Water Resources Control Board: It Should Ensure a More Consistent Administration of the Water Quality Certification Program


Our audit of the State Water Resources Control Board's (state water board) and the regional water quality control boards' (regional water boards) administration of the water quality certification program (certification program) as it relates to the California Department of Transportation (Caltrans) highlighted the following:


The Federal Water Pollution Control Act, commonly referred to as the clean water act, includes requirements designed to restore and maintain the chemical, physical, and biological integrity of the nation's waters. California's Porter-Cologne Water Quality Control Act (water quality act) designates the State Water Resources Control Board (state water board) as the State's water pollution control agency for all purposes of the clean water act. Specifically, the water quality act authorizes the state water board to exercise any powers delegated to the State by the clean water act and authorizes it to make rules and regulations to carry out its powers and duties, including setting state policy for water quality control. The water quality act recognizes that regional differences such as precipitation and topography affect how water quality control should be administered. Under the water quality act, nine regional water quality control boards (regional water boards) coordinate among themselves and with the state water board to protect water quality. Although the regional water boards exercise some autonomy in protecting water quality within their regions, they must adhere to the state water board's regulations and policies.

This audit is of a specific water quality control program—the water quality certification program (certification program). The certification program addresses Section 401 of the clean water act, which requires any entity applying for a federal license or permit to conduct any activity that may result in a discharge of pollutants into federal waters to obtain a water quality certification from the state in which the activity is to occur. For example, performing an activity that requires the dredging or filling of rivers, streams, or wetlands (dredge and fill projects) requires a water quality certification. Typical dredge and fill projects include building bridges, widening roadways, and stabilizing roadway slopes and embankments.1 When the State issues a water quality certification for a project, it is certifying that the project will comply with state and federal water quality laws and regulations. In fact, the federal government cannot issue a license or permit for these activities unless the state where the activities will occur has issued a water quality certification or waived its right to do so.

This audit focuses on the water quality certifications that the California Department of Transportation (Caltrans) has obtained. As the state agency responsible for highway, bridge, and rail transportation planning, construction, and maintenance, Caltrans is required to obtain water quality certifications for many of its projects. For example, if a highway embankment near a water body becomes unstable, Caltrans may need to obtain a water quality certification in order to receive a federal permit that authorizes those repairs. From fiscal years 2007-08 through 2011-12, the water boards issued more than 300 water quality certifications to Caltrans.

In our review of four water boards—the state water board, the North Coast Regional Water Quality Control Board (North Coast), the Central Valley Regional Water Quality Control Board's Redding Office, and the San Diego Regional Water Quality Control Board (San Diego)—we found that the water quality certifications they issued during fiscal years 2007-08 through 2011-12 generally complied with federal and state law. For example, these water boards did not exceed their authority when they added conditions to water quality certifications requiring water quality certification-holders (certification-holders) to protect water quality during construction.

However, the state water board could take additional actions to improve consistency in the certification program. For example, even though the requirements to apply for a water quality certification are the same throughout the State, the water boards use differing application forms for water quality certification, which unnecessarily burdens applicants. The length of the application forms at the state water board and the three regional water boards we visited range from five to 17 pages, as each requires a different level of detail. The state water board said it plans to implement a statewide electronic application form to address the inconsistencies among applications. Additionally, none of the water boards we visited consistently notify applicants regarding the completeness of their applications within 30 days as state laws and regulations require. Of the 41 projects we evaluated, the water boards did not send notifications for 15 within the required time frame—including three that were not sent at all. Although we could not determine whether the missed deadlines delayed the issuance of certifications, applicants such as Caltrans may not be aware that their application is incomplete or that they need to provide more information if they do not receive formal notification of their application status.

Moreover, the water boards have not consistently issued certifications within 60 days of deeming applications complete, which federal regulations require for water quality certifications that are a prerequisite to a dredge and fill permit. Of the 41 projects we reviewed, four certifications were issued more than 60 days after the water boards deemed the application complete. In one instance San Diego did not issue a certification to Caltrans until 129 days after it received a complete application. These delays are the result of the water boards' misunderstandings about the program requirements. Further, one regional water board—North Coast—does not review the accuracy of application fees it collects from Caltrans. As a result, North Coast failed to collect $18,000 from Caltrans for six of the nine application fees that we reviewed. The state water board expects regional water boards to review application fees but acknowledged that it has not specifically directed them to do so.

In evaluating other aspects of the certification program, we found that the state water board needs to assert more effective leadership to address inconsistent monitoring practices at the regional water boards, and it needs to improve its administration practices. Specifically, the regional water boards' inconsistent monitoring practices do not adequately ensure that certification-holders adhere to the conditions of their water quality certifications. As an example, although certifications often require the submission of periodic reports, the regional water boards generally do not track certification-holders' compliance with these requirements. Additionally, the staffing costs that the regional water boards include in penalty actions2 are inaccurate and the regional water boards do not generally support those costs with sufficient documentation. The state water board's enforcement policy encourages the regional water boards to add staff enforcement costs into the penalties they assess, which include the time it takes for staff to validate and document violations and prepare penalty actions as well as to prepare for any necessary hearings. However, two of the three regional water boards could only substantiate staff enforcement costs for five of the 11 penalty actions they issued that included these costs over the past five fiscal years. The other regional water board did not take any penalty actions during this time. Further, the state water board has directed the regional water boards to use a staff cost rate that does not reasonably reflect the costs of the certification program, resulting in an overstatement of estimated staff enforcement costs of $87,000 in one penalty action we reviewed. However, in this case the certification-holder negotiated a settlement so no overpayment occurred.

In reviewing other administration practices at the state water board, we found that it does not adequately track the penalty amounts it receives from water quality certification enforcement activities and, contrary to legislative intent, over the past five fiscal years it has deposited penalty amounts totaling $374,000 into an incorrect account. Once we alerted the state water board to this oversight, it transferred the penalty amounts into the correct account.

Caltrans indicated that working with the nine regional water boards is difficult because they have different ways of administering the certification program. Our review confirmed that inconsistencies exist in the water boards' application process and monitoring efforts, which lends to a perception of differing requirements among them. Caltrans also expressed concern that the regional water boards sometimes exceed their authority under state regulations by adding prescriptive best management practice requirements to water quality certifications. However, the regional water boards we visited use a consistent enforcement process for the certification program and the conditions they added to their water quality certifications did not exceed their authority. Caltrans also asserted that its costs to comply with requirements of the certification program have increased significantly over the last five years. Because it does not track these costs, Caltrans was unable to support its claim.

Finally, the primary database the state water board uses to track water quality certifications—the California Integrated Water Quality System (water quality database)—is incomplete. The reasons are twofold: the state water board has a backlog of over 1,600 documents for certifications that it has not entered into the system as of March 2013, and it has not done enough to ensure that the regional water boards consistently record their monitoring activities and other certification program information in the water quality database. As a result, the public and other stakeholders do not have access to reliable certification program information as the water quality act requires.


The state water board should remind regional water boards of required application processing time frames and notifications and continue with its effort to adopt a single application form.

The state water board should direct North Coast as well as the other regional water boards to verify the accuracy of fees that applicants submit. Additionally, North Coast should take steps to collect the underpaid fees from Caltrans that we identified.

The state water board should direct regional water boards to more consistently monitor compliance with water quality certifications and use the water quality database to track their monitoring efforts.

If regional water boards continue to include staff enforcement costs in penalty actions, the state water board should require the systematic tracking of staff enforcement hours and documentation of cost calculations. Further, it should revise the staff cost rate used in penalty action calculations to reflect actual staff and overhead costs for the certification program.

The state water board should maintain a regular accounting of fines collected on penalty actions.

If Caltrans believes that its costs related to compliance with the certification program are increasing, it should track those costs for a period of time and work with the state and regional water boards to resolve any cost concerns.

The state water board should resolve the backlog for the water quality database and ensure that the regional water boards enter all appropriate certification program information into the system.


The California Environmental Protection Agency and state water board concurred with our findings and recommendations and stated that implementing the recommendations will result in a more accountable and transparent certification program. North Coast acknowledged that the report is consistent with our discussions. Finally, the Business, Transportation and Housing Agency and Caltrans agreed with our conclusions, and Caltrans stated that it recently established a committee to determine the most effective course of action to implement our recommendation.

1 Other construction projects may also require water quality certifications, including building nuclear power plants or hydroelectric projects; however, this audit focuses on dredge and fill projects related to Caltrans.

2 Penalty actions are fines assessed to certification-holders who violate the terms of their water quality certifications.