Mysis relicta can be observed on echograms as a sound scattering layer when they migrate into the water column at night to feed on zooplankton. However, quantitative measures of mysid abundance with hydroacoustics requires knowledge of mysid target strength (TS), a method of removing fish echoes and contribution from noise, and an understanding of the effect of range on the ability of hydroacoustics to detect mysids (the detection limit). Comparisons of paired net data and acoustics data from July 7, 2005 yielded a mysid TS of −86.3 dB (9 mm animal) and a biomass TS of −58.4 dB (g dry wt)−1. With ambient noise levels (Sv of −125 dB at 1 m depth) and this TS, we can detect a mysid density of 1 m−3 at 60 m depth with a signal to noise ratio of 3 dB. We present a method to remove backscattering from both noise and fish and apply this method and the new TS data to whole lake acoustic data from Lake Ontario collected in July 25–31, 2005 with a 120 kHz echosounder as part of the annual standard fish survey in that lake. Mysis abundance was strongly depth dependent, with highest densities in areas with bottom depth > 100 m, and few mysids in areas with bottom depth < 50 m. With the data stratified in five bottom depth strata (> 100 m, 100-75 m, 75–50 m, 50–30 m, < 30 m), the whole-lake average mysid density was 118 m−2 (CV 21%) and the whole-lake average mysid biomass was 0.19 g dry wt m−2 (CV 22%) in July 2005. The CVs of these densities also account for uncertainty in the TS estimates. This is comparable to whole-lake density estimates using vertical net tows in November, 2005 (93 m−2, CV 16%).

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