Size spectra analysis (SSA) is used to detect changes in food webs by simplifying complex community structures through abundance-versus-biomass considerations. We applied SSA to 10 years (2006-2015) of data on Great Lakes organisms ranging in size from picoplankton to macrozooplankton. Summer pelagic size spectra slopes were near the theoretical value of -1.0, but spring slopes were steeper, reflecting seasonal differences in abundance of small and large individuals. Pelagic size spectra slopes were relatively stable over the time period we examined. Height (the predicted number of organisms at the spectra midpoint) varied among lakes and was slightly higher in summer than spring in more productive basins. Including benthic data led to shallower slopes when combined with pelagic data, suggesting benthic organisms may increase food web efficiency; height was less affected by benthic data. Benthic data are not routinely included in SSA, but our results suggest they affect slopes and therefore SSA-based predictions of fish abundance. The ability of SSA to track changes in trophic energy transfer makes it a valuable ecosystem monitoring tool.