Hydroacoustic methods are routinely used for fish population assessment and monitoring in lakes and reservoirs around the world and are particularly embedded in European and North American lake management. However, the comparability of hydroacoustic results can be difficult to assess due to the large number of variables (sound frequency, sound pulse duration, system manufacturer, analysis method, etc.) that can influence acoustic estimates. This study investigates the effect of variations in analysis method and hydroacoustic system on commonly produced outputs. Volume backscattering strength (S-v), mean target strength (TS), fish abundance, and biomass were estimated using two analysis methods (echo integration and track-counting) using data recorded from a large, deep lake (Windermere, UK) by four vertically oriented split-beam systems operating at three sound frequencies (120 kHz, 200 kHz, and 400 kHz). The two analysis methods used produced similar estimates of fish abundance and fish biomass. We therefore concluded that echo integration and track-counting can be robustly used and outputs justifiably compared under the conditions of the Windermere surveys. In addition, we compared mean S-v, mean TS, fish abundance, and biomass estimates across the four hydroacoustic systems. The only significant result was for abundance estimates, however, the system made a small contribution to the overall variability. All four systems provided similar results for the other metrics, demonstrating that independent hydroacoustic surveys operating within the European Standard can make a major contribution to the assessment and monitoring of fish populations in deep lakes and reservoirs.