This paper describes in depth the design and application considerations of a computer based measurement system enabling 1 MS/s simultaneous sampling of 47 hydrophones for cross sectional recordings of echolocation beams of toothed whales (Odontocetes). An earlier prototype version of the system has previously only been presented as a brief proof of principle that did not offer a complete description of the software and hardware solution. Crucial hardware and software design considerations of the further developed system include the re-arm times of the burst mode sampling and the dual-core distributed execution of the software components. The rearm time was measured to 283 μs, using a 550 μs long sample window around each click. This enables burst mode sampling of clicks with an inter-click interval as short as 833 μs. It is shown through both synthetic benchmark tests of the system and through field measurements of bottlenose dolphins (Tursiops truncatus) and a beluga whale (Delphinapterus leucas) that it is capable of acquiring, analyzing and visualizing data in run-time. It operates effectively also in highly reverberant surroundings like concrete pools and shallow waters. Burst mode sampling allows the system to block reflections with 0.3 - 0.5 m longer propagation paths than the direct path. It is suggested that the system’s compliance to reverberant recording sites makes it valuable in future dolphin echolocation studies.