Assessments of changes in the ecological state of aquatic ecosystems are always burdened with uncertainty, which results from environmental reasons and poor repeatability of measurement results of elements enabling the assessment. This study determines the uncertainty related to the elements of the assessment of the hydroacoustic structure of fish communities’ (1) vertical target strength distribution (TS) in two-meter layers of water and (2) changes in the area where fish were recorded (which was determined on the basis of maps of their distribution in 2 m deep water layers). The object of this study was a lake (depth: 27 m) in which at the end of June 2016 the O2 concentration was <1.4 mg L−1 below 8 m depth, which resulted in the accumulation of fish to a depth of 6 m. Hydroacoustic acquisition was carried out along transects arranged in the east–west (WE), north–south (NS), and zigzag (ZZ) directions in three repetitions. It was shown that the empirical probability of obtaining statistically different results was 2/9 when (1) Kendall’s τ coefficient, used to determine the similarity of the TS distribution, was less than 0.7—moderate correlation—and (2) fish occurrence areas in two cases (WE and ZZ on the third day of research) in layers 2–4 m and 4–6 m differed statistically significantly from the average area for all repetitions by 10–14% and 56–66% (p < 0.05), respectively. The obtained results indicate quite good repeatability of acoustic measurements; however, in order to reduce the uncertainty, it is recommended that tests be conducted in this type of lake in three series of measurements.