The fatty acid compositions of phytoplankton and major primary consumers were analyzed during the development of seasonal algal blooms in the Bahia Blanca estuary, situated on the southern coast of the province of Buenos Aires (Argentina), and Trinity Bay, at Sunnyside, on the eastern coast of Newfoundland (Canada). Primary consumers in the Bahia Blanca estuary were zooplankton dominated by the calanoid copepod Acartia tonsa. At Sunnyside, the primary consumers were the sea scallop Placopecten magellanicus, an ecological and economical important benthic bivalve. The study shows that in spite of obvious differences between the two environments and the analytical approaches employed in each case, the analyses of fatty acid biomarkers can provide relevant ecological information. The fatty acid composition of the lipids of Bahia Blanca phytoplankton (high concentrations of the fatty acids 14:0, 16:4ω1, and 20:5ω3) reflected the presence of diatoms as a major component throughout the bloom. Fatty acid markers of the post-bloom phytoplankton in Bahia Blanca indicated a decline of phytoplankton biomass, and a relatively high input of detritus and terrestrial plant materials to the particulate organic matter of the estuary. Linoleic acid (18:2ω6), a typical “terrestrial” fatty acid, was conspicuous in the lipids of the post-bloom particulate matter of the Bahia Blanca estuary; 18:2ω2 was subsequently incorporated into zooplankton lipids diatom markers were also prominent in the lipids of pre-bloom and bloom phytoplankton at Sunnyside; post-bloom phytoplankton showed higher proportions of 18:0, 18:1ω9, and 18:4ω3, characteristic and often major fatty acids of dinoflagellates. The fatty acids of the digestive gland of P. magellanicus reflected the fatty acid composition of the phytoplankton, whereas those of the adductor muscle were practically unaffected by the composition of the food. This organ-specific response of an animal to the fatty acid composition of the diet is examined in terms of different applications of the fatty acid marker concept.