Volunteers collect samples once a month throughout the year. Samples are collected by lowering a net into the water to collect a sample at the north T-Pier near the Coast Guard/Harbor Patrol station in Morro Bay. Volunteers then conduct taxa counts under the microscope and identify plankton down to the genus level. The datasheet and a preserved sample are sent to the California Department of Public Health (CDPH) to assist with biotoxin monitoring to ensure the safety of farmed and sport harvested shellfish for human consumption. This effort was started in conjunction with CDPH in 2002.

Toxic blooms occasionally occur in Morro Bay. These blooms are detected during weekly pulls by the oyster farmers and/or by twice monthly pulls conducted by the MBNEP. All data is shared with CDPH. If CDPH feels there are signs of a bloom, they will ramp up monitoring efforts. This includes increasing the frequency of phytoplankton pulls and analysis of shellfish meat for biotoxins.

Out of a total of 219 plankton pulls in Morro Bay (from 2002 through 2012), there have been 138 pulls containing Pseudo-nitzschia, the species known to produce domoic acid, and 23 pulls with Alexandrium, the species potentially containing paralytic shellfish poison toxins.