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1 Side-looking (SL) deployment of hydroacoustic transducers is an effective approach to manage the issue of the near-field effect that limits abundance estimation of fish near the surface (<2 m) when using down-looking (DL) deployment in acoustic surveys. However, determining appropriate target strength (TS) thresholds for SL is more difficult due to the greater variability of orientation of fish and thus greater variability in the TS compared to DL. In this paper, I derive appropriate TS thresholds for SL acoustics in two alewife (Alosa pseudoharengus) dominated lakes, one in New York and the other in Pennsylvania. I use ex situ TS distribution of alewife from a net cage experiment as well as in situ TS distribution of alewife from the lakes to determine the appropriate TS thresholds. With the thresholds applied, I explore the feasibility of using SL deployment as a fisheries assessment technique by comparing fish density estimates of SL with DL and multimesh vertical gill nets. DL and SL acoustic surveys were conducted at Cayuta Lake in October 13, 2008 and October 29, 2007, and at Silver Lake in October 14, 2008. In addition, vertical gill nets were set in the lakes for length (mm), weight (g), and distribution in the top 6 m. Ex situ net cage experiments were conducted in 2006 at Oneida Lake using 5 alewives. Results from the net cage experiment shows a TS distribution that is both wide and skewed to the right with more targets observed that are greater than −55 dB compared to in situ TS distributio