Developing the crustacean zooplankton community size spectrum into an indicator of change in lakes requires quantification of the natural variability in the size spectrum related to broad-scale seasonal, annual, and spatial factors. We used a random effects model to measure monthly, annual, and inter-lake variability in the slope and centered height of the crustacean zooplankton normalized abundance size spectrum (NASS) from 1981 – 2011 among eight Canadian Shield lakes. The slope was a relatively stable characteristic of the zooplankton community compared with the height, which varied significantly among lakes. We identified a seasonal signal in height and slope and used a mixed effects model to characterize the linear rate of change from May to October: there was an overall decline in height and an overall increase in slope. Seasonal variance was greater than annual variance for both the height and the slope, suggesting that long-term monitoring of lakes and inter-lake comparisons using zooplankton size spectra should be based on temporally standardized sampling protocols that minimize the effects of seasonal processes.