The coastal waters of the West Antarctic Peninsula (WAP) are associated with large phytoplankton blooms dominated by large (>20 microns) diatoms however, nanoplankton (<20 microns) are also an important component in the phytoplankton community. The dominant nanoflagellate in the WAP has been suggested to be cryptomonad algae. Using a twenty-year time series collected by the Palmer Long Term Ecological Research (Pal LTER) program at the United States Palmer Research Station, we assessed long-term patterns and stability in the coastal phytoplankton communities in the WAP. There was significant interannual variability in the integrated water column chlorophyll a (chl-a) concentrations, which varied by a factor of 5 over the 20-year time series. Within the time series the dominant phytoplankton taxa were diatoms, with the second most abundant phytoplankton taxa present being cryptophyes. Peak biomass was observed in summer months mirroring declines in the seasonal monthly average wind speed. Cryptophytes were most abundant in the summer months of December and January after the seasonal retreat of sea ice. While diatoms were observed over the full range of observed salinities (34.5 to 32) as well as over the full range of in situ temperatures (-1.5 to 2.5° C), the cryptophyte populations were observed in lower salinity (33.75 to 32.5) and colder water (-1 to 1° C). Time series showed that during years when environmental factors favor water column stability, there are anomalously large summer diatom blooms that resulted in high krill recruitment, consistent with the classic Antarctic paradigm of a short diatom−krill−top predator food chain. In low phytoplankton biomass summers there was a recurrent shift to a larger proportion of the overall chl-a being present in cryptophytes. Consistent with modeling studies this suggests a potential shift to multivorous food web, which has significant ecological and biogeochemical implications, such as decreased efficiency of atmospheric carbon sequesteration.