Recently the fishing vessel has been widely used to collect acoustic data to provide information on the distribution and abundance of Antarctic krill (Euphausia superba). One basic assumption of the acoustic survey is that the effective range detection limit (RDL) of the echo sounder could cover the major distribution layer of Antarctic krill. However, due to the lack of noise mitigation design, the background noise levels of fishing vessel are usually higher than the research vessels, which may seriously degrade the RDL of the echo sounder system. In order to facilitate the use of fishing-vessel-based acoustic data, in the present study, a method was introduced to estimate the RDL of scientific echo sounder based on the background noise estimates obtained using post-processing technique. Furthermore, taking the Antarctic krill fishing vessel “Fu Rong Hai” as a case study, the background noise levels and RDLs of the Simrad EK 60 echo sounder system (38, 70 and 120 kHz) onboard were estimated at various vessel speeds. Results indicated that the RDL was not only related to echo sounder specifications and backscattering strength of the survey target, but also to the background noise level and the vessel speed. For “Fu Rong Hai”, the background noise levels of the acoustic data collected by the EK60 system increased markedly with increasing vessel speed and resulted in decreased RDLs for all the three frequencies. At a vessel speed of 8 kn and a signal-to-noise ratio (SNR) of 10 dB, the RDLs for all the three frequencies were estimated to be larger than 300 m for the Antarctic krill with a S_v threshold of −70 dB , while the RDL decreased to be around 100 m at 70 kHz which could not meet the requirement of depth coverage (250 m) for Antarctic krill acoustic survey when the vessel speed was increased to 12 kn. The results proved that the vessel speed may have significant impact on the performance of effective range detection limit of echo sounder system, and this study may provide valuable reference for the use of fishing vessels to conduct acoustic survey particularly the vessel speed and data processing.