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Three-dimensional modeling of lake morphometry enables the calculation of lake volume, planar surface area, and basin surface area, which are critical components of a conceptual model of how planktic and benthic habitat areas change with changing lake level. We have applied three-dimensional modeling to Foy Lake, Montana, and compared model results of changing ratios of planktic and benthic habitat areas at all possible lake levels to sediment cores recovered from the lake. The model allows us to produce semiquantitative depth reconstructions and greatly improves lake-level reconstruction of this morphometrically complex basin. The conceptual model also was modified to examine the influence of resuspension versus gravity redistribution of diatomaceous material on the sedimentary record. Comparison of the model results with both long and short sedimentary records from Foy Lake, Montana, suggests that planktic : benthic ratios may be a better predictor of mean lake depth than maximum lake depth. The model developed here is simple enough to be easily implemented, has few requirements, can be adapted to suit any lake basin, and can be augmented to examine a variety of different lake processes that affect habitat availability.