Algal carotenoids (n:16) and chlorophylls (n:7) were determined in phytoplankton (n:60), filamentous algae (n:14) and sediments (n:44), collected from two nearshore sites in eastern Lake Erie (Van Buren Point (VBP), 6.5 m; Point Gratiot (PG), 17 m), during summer and fall of 2003, 2004 and 2005. The most prominent biomarkers for diatoms (fucoxanthin), cryptophytes (alloxanthin), chlorophytes (chlorophyll-b) and cyanobacteria (zeaxanthin) revealed temporal variations in phytoplankton community composition, which were correlated to water temperatures: i) seasonal succession, from diatoms with some cryptophytes in June (cool), to an increased percentage of chlorophytes and cyanobacteria in August and September (warm); ii) differences between 2004 (cool; cryptophytes more abundant) and 2005 (warm; chlorophytes more abundant). Filamentous algae (chlorophytes, epiphytic diatoms; some cyanobacteria) varied in condition, according to levels of chl-a, pheopigments, and class biomarkers: high, at VBP (growing; decaying; bont/E suspect); low, at PG (mostly dead). Relative to phytoplankton, sediments were depleted in several biomarkers (chl-a; diadino-, neo- and violaxanthin) but enriched with others, particularly at PG (pheopigments; diatoxanthin; canthaxanthin, echinenone; alloxanthin). Sediment composition was characterized by strong differences between sites (chl-a, chl-b and fucoxanthin nearly 10-fold greater at VBP than PG) and increasing accumulation of biomarkers from year-to-year. A linear log-log function, relating total carotenoids to total chlorophylls (intercept -0.516, slope 1.054, r² 0.96), implied increased biodegradation among specimen types: levels of pigments (pmol/g ww) decreased three orders of magnitude, from phytoplankton, through filamentous algae, to sediments. Deviation from a 1:1 relationship indicated 1.7-fold depletion of carotenoids relative to chlorophylls at mid-range.