Multibeam water column image (WCI) has high application value in underwater target detection and recognition. However, it is often affected by receiver beam side lobe, the third-party sonar interference, and complex marine environment noise, such as marine organism, suspended solids, microbubbles and so on, which brings a great impact on its applications. Therefore, this paper proposes a comprehensive method to suppress those interferences in WCI. Firstly, the origin and mechanism of the interferences have been fully analyzed. In accordance with the characteristics of spatial distribution of those interferences, an abnormal "arc" detection and elimination method based on the features of intensity distribution is proposed, which aims to suppress the abnormal "arc" mainly caused by receiver beam side lobe. In this process, a target remaining principle is set to remain the target fragments existing in the abnormal "arc". Secondly, a background noise reduction method based on image intersection and difference set is proposed, which aims to suppress the background noise mainly caused by marine organism and suspended solids. Combined these two methods, a comprehensive method is obtained. The experimental results show that these methods can suppress the interference in WCI efficiently. The quality of the WCI is highly improved and the targets in WCI are remained.