The paper describes the performance calibration and use of a 90‐deg sector scanning sonar for the collection and extraction of information on the 3D structure of fish schools. The equipment, which consists of a 455‐kHz 60‐beam sector scanning sonar linked to a PC is described briefly. The specific calibration problems of a high‐frequency instrument with multiple beams is discussed and calibration data from on‐axis and beam shape measurements are presented. The deployment of the instrument for data collection at sea and the data collection methods are described. Examples of the data collected are given. A three‐dimensional data processing algorithm is presented along with results of reconstruction from selected schools. The statistical properties of within school data are discussed along with indications of the precision of internal structures that can be evaluated using the sonar. The development of this system is supported by the European research program, AIR.