DWRLB houses CDPH environmental microbiology services and expertise in the Microbiology Unit (MU). The M​​​U is accredited by The NELAC Institute (TNI​) to perform microbiological water testing mandated by the federal Clean Water Act. 

The MU specializes in detection of environmental pathogens and indicator organisms in water and wastewater matrices. The unit is part of the CA Surveillance or Wastewater (CalSuWers) program in CDPH, which is designated as a Center of ​​Excellence by the CDC National Wastewater Surveillance System (NWSS​) national program. The MU provides wastewater-based epidemiology (WBE) molecular testing and genomic sequencing for infectious disease monitoring of SARS Cov-2, influenza, RSV, MPOX and other pathogens in the wastewater to complement patient case incidences. 

The MU is a CDC ELITE​ certified environmental testing laboratory targeting legionella spp. for outbreak response monitoring and manage​​s a certified testing program for harmful algal bloom (HAB​) toxin monitoring for biological cyanotoxins in impacted surface and drinking water environments. The MU also served as the technical lead research lab in a special study with San Diego County Public Health (SDPH) that led to the first certified molecular-based rapid detection method in the U.S. for regulatory monitoring of fecal indicator bacteria, enterococcus spp., in coastal waters. The method is currently used by SDPH for daily water quality reporting and public notifications.