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1. Emergence traps were set overnight on the sediment surface to sample the littoral microcrustaceans of 22 Canadian Shield lakes that ranged in pH from 4.56 to 6.92. Traps were randomly allocated in quintuplicate in both wave-washed sandy habitats where pipewort ( Eriocaulon septangulare) was the dominant macrophyte (termed pipewort habitats), and more protected habitats dominated by floating-leaved macrophytes (termed floating-leaved habitats). 2. In total, 50 cladoceran and 22 copepod species were found, with 16–45 species in each lake. Lakes that had never acidified exhibited a more diverse fauna than lakes that had acidified. 3. There were only minor differences between the numbers of species found in floating-leaved versus pipewort habitats except for one lake. Non-chydorid cladoceran, chydorids and copepods constituted 45%, 26% and 29% of the total number of individuals, respectively. 4. Based on presence/absence, dominance scores and frequency of occurrences of species, the microcrustacean faunal composition was similar in the two habitats. A detrended correspondence analysis confirmed that there was no separation between the two main types of habitat, and that pH was the parameter most strongly correlated with the dominant microcrustacean compositional gradient among lakes. [ABSTRACT FROM AUTHOR]