ABSTRACT. The seasonal v d r~a t~o nIn the coniposltlon of algal communltles In the lower St. Lawrence Estuary was examined uslng MPLC plgments and cell taxonomy, and the effic~ency of these 2 techn~ques was compared A malor centric d~a t o m bloom was observed In July 1992, preceded by an Increase In pennate d~atoms in June, l~kely caused by bottom resuspenslon due to sprlng runoff. G r a z~n g In June and July was ~n d~c a t e d by the presence of pyropheophorblde a, a copepod grazing product tracer, dnd chlorophyll degrad a t~o n plgments, l~kely assoc~ated w~t h sloppy feedlng and w~t h the presence of cells (d~atoms) wlth hlgh chlorophyllase actlvity and ac~dic cell sap. Var~ous pheopigments and degradation products of chl a \vere found In these 2 months. T h~s 1s cons~stent ivlth observat~ons of maximum abundances of major copepod specles and of herb~vorous clllates In June preceding the summer d~a t o m bloom. May was character~zed by nanoflayellates from Chrysophyceae, C~yptophyceae and Chlorophycede, lower values of algal biomdss and production and h~g h e r l~g h t harvesting effic~ency M~xlng prevented the establ~shment of vertical fluorescence patterns in May and September and probably lowered the effectwe daily light exposure of algae, w h~c h translated Into lower light accl~mat~on than In summer and h~g h e r ratios of photosynthet~c plgments to chl a. Low-l~ght acclimatlon was also observed In the deep (>20 m) June and July populat~ons, affecting marker plgment coeff~c~ents used to calculate relat~ve algal contribut~ons. Increases In relatlve amounts of chlorophyll~de a and In the allomer of chl a in September were ~nterpreted as slgns of algal senescence. The September populat~ons were coniposed of d number of chlorophyte and chrolnophyte (fucoxanth~n-conta~n~ng) algae. LOW p~gment concentratlons and lo\v numbers of observat~ons con~pl~cated the ident~f~cation task for that month. Plgment and rnlcroscoplc approaches were compared on the b a s~s of ( l ) cluster~ng, uslng each separately, (2) correlat~ons between pigments and cell groups, and (3) transformation of plgment data Into algal group contr~but~ons to chl a. The 2 approaches generally gave s~l n~l a r results even though they showed ddferent charactel-~st~cs the presence of