We present a novel framework for analysis and visualization of fish schools in 3D sonar surveys. The 3D sonar technology is new and there have not been applications to visualize the data in 3D. We have created an application called Sonar Explorer that satisfies the requirements of domain scientists. Sonar Explorer provides easy and intuitive semi-automatic fish school tracking and survey map generation. The overall pipeline is described and all pipeline stages relevant for visualization are highlighted. We present techniques to deal with 3D sonar data specifics: highly anisotropic volume data aligned on a curvilinear grid. Domain scientists provide initial impressions on interaction and outlook. Categories and Subject Descriptors (according to ACM CCS): I.3.3 [Computer Graphics]: Picture/Image Generation