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 distribution at Cayuta Lake and Silver Lake. SL deployment at Cayuta Lake and Silver Lake observed more targets per km than DL deployment. The catches of alewife in the gill nets at Cayuta Lake in 2008 and 2007 were unevenly distributed with a greater proportion of alewife, both young-of-the-year (YOY) and adults, caught in the top 2 m. Catches of alewife in Silver Lake were more evenly distributed with an equal proportion of YOY alewife caught between 0-6 m, whereas the adults were only caught between 0-4 m. Hydroacoustic and vertical gill net abundance comparisons shows a positive correlation between gill net catch/hr with SL acoustics. However, the correlation between gill net and DL acoustics is negative. I conclude that this study demonstrates the importance of using SL and DL deployment of transducers in abundance estimation. Traditional gear like vertical gill nets should also be used in order to obtain accurate assessment of species and size structure. Further study of the TS distribution of alewife in net cages using SL deployment is needed to improve the determination of the appropriate TS thresholds for data analysis.