Models of ocean colour rely on information about phytoplankton absorption, which varies according to community composition and photoacclimation. Here we show that pigment packaging, which is strongly determined by the size structure of local algal populations, represents a dominant factor in the Estuary and Gulf of St. Lawrence, accounting for ~50%–80% of the reduction in phytoplankton absorption at 440 nm during the spring bloom periods and for 24%–48% before and after the blooms. This is consistent with the importance of diatoms in this environment. Comparison between three methods of estimating packaging gave average values within less than 20% of each other during the blooms. Changes in pigment composition, which also affect phytoplankton absorption, were more important outside bloom periods (particularly in the Gulf), although this influence was relatively modest (11%–13%). This was accompanied by an increase in photoprotective pigments and an absorption peak in the ultraviolet range (~330 nm). Regional variations in phytoplankton absorption reflected bloom conditions, whereas detrital particulate material was highest in the upstream Saguenay region (often more than 60% of the absorption of total particulate material at 440 nm (ap(440))) and was at least 20%–30% elsewhere. This information is a first step towards the development of regional models of ocean colour.

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