The spatial heterogeneity of four macrozooplankton species (Skistodiaptomus oregonensis, Mesocyclops edax, Diaphanosoma brachyurum, and Daphnia sp.) was investigated over different scales, (fine and coarse scales: 2–40 m; lake-size scale: 10–380 m) in a small Canadian Shield lake. Values for the log s2: log [Formula: see text] relationships were established for the different scales and compared. Spatial analysis methods (space-constrained clustering analysis, spatial autocorrelation, and variogram modelling) were used for describing the surface distribution patterns observed on the whole-lake transect. The study demonstrated that spatial heterogeneity occurs on both the fine and coarse scales. Maximal spatial heterogeneity was observed on the vertical axis (depth) rather than on the horizontal axis. Macrozooplankton patchiness scales in Lake Cromwell correspond to whole-lake scale patterns for M. edax and D. brachyurum, and to fine-scale patterns for S. oregonensis and Daphnia spp. Our results confirm the general trend of interspecific variations in patch sizes of freshwater macrozooplankton. Distribution of the invertebrate predators Chaoborus spp. is inversely related to the large-scale gradient of D. brachyurum. Multiple regression analysis showed that several physical (water temperature, oxygen, wind direction) and biological (chlorophyll a) factors, in addition to mean population abundance, were correlated with macrozooplankton heterogeneity on the fine scale.