A substantial amount of water quality testing takes place at Upper Newport Bay. Much of it is performed for regulatory compliance purposes.
Bacterial testing is performed by the Orange County Health Care Agency Water Quality Laboratory at the Back Bay Science Center. Reports can be found at http://www.ocbeachinfo.com.
Another good source of information is Clean Water Newport.
Several local schools perform bacteria and other water quality testing at Upper Newport Bay as part of the Surfrider Blue Water Taskforce.
OC Watersheds performs various water quality monitoring and testing pertaining to sediment, toxics, nutrients, etc.