Raw DNA and RNA V4 tag sequences include samples from the surface at Santa Catalina Island, the Port of Los Angeles, and the San Pedro Ocean time series station (SPOT). Additionally, the SPOT station samples include subsurface chlorophyll maximum, 150m (oxycline) and 890m. We incorporated RNA sequencing into standard 18S rRNA gene sequence surveys with the purpose of assessing those members of the protistan community contributing to biogeochemical cycling (active organisms), using the ratio of cDNA (reverse transcribed from total RNA) to 18S rRNA gene sequences within major protistan taxonomic groups.