Gradient analyses of 29 chemical and physical (C–P) variables and diatom remains in surface sediments of 63 New England lakes (pH 4.4–7.9) indicate a primary C–P gradient of pH, alkalinity, Ca, Mg, conductance, and Al; diatom distributions are most strongly related to that gradient (especially to pH and alkalinity) and also reflect secondary gradients (oceanic–inland, lake morphology, and regional chemistry). The primary relationship supports the calibration of regression models for paleolimnological inference of pH and alkalinity based on diatoms. To optimize inference models for the region's most acidic lakes, a second set of calibrations was run after culling the seven least acidic lakes. Diatom distributions on the restricted pH and alkalinity gradients are of two types: roughly uniclinal and variously unimodal. Models assuming each type were calibrated: CLUSTER (linear), DCA (unimodal), and CCA (unimodal). Log-transformation of alkalinity improved the 63-lake DCA and CLUSTER regressions, but worsened or left the others unchanged. Postulated causes of incongruous diatom assemblages and outlier pH and alkalinity inferences are sediment mixing, focusing time lag, growth of epipelic diatoms at the core site, and atypical lake morphology. Careful selection of calibration lakes is at least as important as the choice of regression models.

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