We measured variability in the composition of diatom and chrysophyte assemblages, and the pH inferred from these assemblages, in sediment samples from Big Moose Lake, in the Adirondack Mountains of New York. Replicate samples were analyzed from (1)a single sediment core interval, (2) 12 different intervals from each of 3 separate cores, and (3) 10 widely spaced surface sediment samples (0-1 cm). The variability associated with sample preparation (subsampling, processing, and counting) was relatively small compared to between-core and within-lake variability. The relative abundances of the dominant diatom taxa varied to a greater extent than those of the chrysophyte scale assemblages. Standard deviations ofpH inferences for multiple counts from the same sediment interval from diatom, chrysophyte, and diatom plus chrysophyte inference equations were 0.04 (n = 8), 0.06 (n = 32), and 0.06 (n = 8) of a pH unit, respectively. Stratigraphic analysis of diatoms and chrysophytes from three widely spaced pelagic sediment cores provided a similar record of lake acidification trends, although with slight differences in temporal rates of change. Average standard deviations of pH inferences from diatom, chrysophyte and diatom plus chrysophyte inference equations for eight sediment intervals representing similar time periods but in different cores were 0.10, 0.20, and 0.09 pH unit, respectively. Our data support the assumption that a single sediment core can provide an accurate representation of historical change in a lake. The major sources of diatom variability in the surface sediments (i.e., top 1.0 cm) were (1) differences in diatom assemblage contributions from benthic and littoral sources, and (2)the rapid change in assemblage composition with sediment depth, which is characteristic of recently acidified lakes. Because scaled chrysophytes are exclusively planktonic, their spatial distribution in lake sediments is less variable than the diatom assemblages. Standard deviations ofpH inferences for 10 widely spaced surface sediment samples from diatom, chrysophyte and diatom plus chrysophyte inference equations were 0.21, 0.09, and 0.16 of a pH unit, respectively. 268