Water samples for the analysis of pigments using High Performance Liquid Chromatography (HPLC) were collected only in the first 12 months of the sampling program. Pigment analysis is used to estimate algal community composition and concentration. Pigments which relate specifically to an algal class are termed marker or diagnostic pigments. Some of these diagnostic pigments are found exclusively in one algal class (e.g. prasinoxanthin in prasinophytes), while others are the principal pigments of one class, but are also found in other classes (e.g. fucoxanthin in diatoms and some haptophytes; 19′-butanoyloxyfucoxanthin in chrysophytes and some haptophytes). The presence or absence of these diagnostic pigments can provide a simple guide to the composition of a phytoplankton community, including identifying classes of small flagellates that cannot be determined by light microscopy techniques. There was general similarity in pigment composition between all sites, with a presence of diatoms (as indicated by fucoxanthin), haptophytes (hex-fucoxanthin), prasinophytes (prasinoxanthan), cryptophytes (alloxanthan), cyanophytes (zeaxanthan) and green algae (chl-b) in nearly all monthly samples at all sites. The green algae could be in the form of euglenophytes or prasinophytes; the absence of the pigment lutein in all samples indicates that chlorophytes are not present in Storm Bay, at least at the sites sampled.

Chlorophyll a concentration is widely used as a proxy to describe trends in phytoplankton biomass over spatial and temporal scales. The concentration of chlorophyll a in Storm Bay showed surprisingly little variation across the seasons. There was a gradient in concentration from site 1 to site 3, where chlorophyll a decreased slightly. It was highest and most variable at the inshore sites 1 and 9, and lowest at site 3, furthest out in the bay. There was no clear annually recurrent seasonal bloom, although data suggests higher values in spring and autumn (see later time series).