Hydroacoustics can be used to assess zooplankton populations, however, backscatter must be scaled to be biologically meaningful. In this study, we used a general model to correlate site-specific hydroacoustic backscatter with zooplankton dry weight biomass estimated from net tows. The relationship between zooplankton dry weight and backscatter was significant (p < 0.001) and explained 76% of the variability in the dry weight data. We applied this regression to hydroacoustic data collected monthly in 2003 and 2004 at two shoals in the Apostle Island Region of Lake Superior. After applying the regression model to convert hydroacoustic backscatter to zooplankton dry weight biomass, we used geo-statistics to analyze the mean and variance, and ordinary kriging to create spatial zooplankton distribution maps. The mean zooplankton dry weight biomass estimates from plankton net tows and hydroa-coustics were not significantly different (p = 0.19) but the hydroacoustic data had a significantly lower coefficient of variation (p < 0.001). The maps of zooplankton distribution illustrated spatial trends in zooplankton dry weight biomass that were not discernable from the overall means.