The large variation in size and shape in diatoms is shown by morphometric measurements of 515 benthic and pelagic diatom species from the Baltic Sea area. The largest mean cell dimension (mostly the apical axis) varied between 4.2 and 653 μm, cell surface area between 55 and 344,000 μm2, and cell volume between 21 and 14.2 × 106μm3. The shape‐related index, length to width ratio, was between 1.0 and 63.3 and the shape‐ and size‐related index, surface area to volume ratio, was between 0.02 and 3.13. Diatom community analysis by multivariate statistics is usually based on counts of a fixed number of diatom valves with species scores irrespective of cell size. This procedure underestimates the large species for two reasons. First, the importance of a species with higher cell volume is usually larger in a community. Second, larger species usually have lower abundances and their occurrence in the diatom counts is stochastic. This article shows that co‐occurring small and large diatom species can respond very differently to environmental constraints. Large epiphytic diatoms responded most to macroalgal host species and small epiphytic diatoms most to environmental conditions at the sampling site. Large epilithic diatoms responded strongly to salinity, whereas small epilithic diatoms did so less clearly. The conclusion is that different scale‐dependent responses are possible within one data set. The results from the test data also show that important ecological information from diatom data can be missed when the large species are neglected or underestimated.

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High-quality calibration data sets are required when diatom assemblages are used for monitoring ecological change or reconstructing palaeo-environments. The quality of such data sets can be validated, in addition to other criteria, by the percentage of significant unimodal species responses as a measure of the length of an environmental gradient. This study presents diatom-environment relationships analyzed from a robust data set of diatom communities living on submerged stones along a 2,000 km long coastline in the Baltic Sea area, including 524 samples taken at 135 sites and covering a salinity gradient from 0.4 to 11.4. Altogether, 487 diatom taxa belonging to 102 genera were recorded. Detrended canonical correspondence analysis showed that salinity was the overriding environmental factor regulating diatom community composition, while exposure to wave action and nutrient concentrations were of secondary importance. Modeling the abundances of the 58 most common diatom taxa yielded significant relationships with salinity for 57 taxa. Twenty-three taxa showing monotonic responses were species with optimum distributions in freshwater or marine waters. Thirty-four taxa showing unimodal responses were brackish-water species with maximum distributions at different salinities. Separate analyses for small (cell biovolume <1,000 lm 3 ) and large ( ‡1,000 lm 3 ) taxa yielded similar results. In previous studies along shorter salinity gradients, large and small epilithic diatom taxa responded differently. From our large data, we conclude that counts of large diatom taxa alone seem sufficient for indicating salinity changes in coastal environments with high precision.