Since most environmental testing procedures require certification or approval from certifying organizations, laboratories must undergo certification processes on a routine basis. The certification process usually consists of a systems audit to qualitatively evaluate the operational details of the laboratory's quality systems. In addition, the laboratory must also routinely analyze proficiency evaluation samples so the outputs of the laboratory's various measurement systems can be assessed.

Many states require that the laboratory be certified by the appropriate state agency before the agency will accept data from that laboratory. In some cases, federal agencies may also require laboratory certification or approval by one of their entities. For example, under the Safe Drinking Water Act, every state is required to have a certification program for laboratories wishing to perform drinking water analyses on samples from that state. Because no two certification programs are the same, this leads to confusion and expense for laboratories and their clients.

In 1995, the National Environmental Laboratory Accreditation Conference (NELAC) was created with the long-term goal of establishing a national accreditation program; however, this program is still not accepted by all states. As of 2008, only 13 states are recognized as NELAC-accrediting organizations.

Many certifications are by method, matrix, and analyte, so always check with your laboratory to ensure it has the needed certification for each test, matrix, and analyte for your project.