ABSTRACTEpiphytic, epilithic, and surface sediment diatom assemblages were identified and enumerated from 35 study ponds on CapeHerschel (78°37″N, 74°42″W), east‐central Ellesmere Island, Canada. All the sites are shallow (maximum depth<2 m), clear, oligotrophic, and freshwater. The ponds freeze completely for 10 months of the year. Major ion concentrations are relatively similar among the 35 sites, although environmental gradients exist. Over 130 diatom taxa from 28 genera were identified in the periphyton samples. Marked differences in species composition were evident among the ponds. Moreover, many of the diatoms exhibited varying degrees of microhabitat specificity. Variance partitioning by canonical correspondence analysis showed that 26% of the total variance exhibited by diatom species composition could be accounted for by the measured environmental variables (i.e. 10.2% by habitat and 15.8% by water chemistry). Pondwater alkalinity best explained the distribution of taxa, and weighted averaging regression and calibration were used to develop a transfer function to infer pondwater alkalinity from the diatom assemblages. Other important environmental variables included [Na+] for the epilithic and [SiO2] for the epiphytic asse