An acoustic Doppler system comprising: an acoustic subsystem controller comprising a digital circuit operatively connected to a plurality of acoustic transceivers; wherein a first acoustic transceiver of the plurality of acoustic transceivers is operatively connected to a first multi element transducer array mounted on an aquatic sensor platform and operated at a first acoustic frequency; and wherein a second acoustic transceiver of the plurality of acoustic transceivers is operatively connected to a second group of at least one transducer mounted on the aquatic sensor platform and operated at a second acoustic frequency different than the first acoustic frequency; characterized in that the digital circuit is configured to: receive a first analog signal from each transducer of the first group of at least one transducer; repeatedly sample the first analog signal with a periodic delay between repetitions, the periodic delay being an integer number of periods of the respective acoustic frequency of the respective acoustic transceiver operatively connected to the respective transducer, wherein each sample constitutes a pair of values separated by one quarter of the period of the first acoustic frequency; receive a second analog signal from each transducer of the second group of at least one transducer; sample the second analog signal; process the pairs of values as components of Doppler velocity estimates, the members of the pairs representing the cosine and sine components of a Doppler-shift signal; and wherein the first acoustic transceiver is operatively connected to the first multi-element transducer array adapted to measure three dimensional motion within a first volume of the aquatic environment with at least four beams; wherein the second acoustic transceiver is operatively connected to the second group of at least one transducer adapted to measure range to an object within a volume of the aquatic environment angularly coincident with the first volume. an acoustic subsystem controller comprising a digital circuit operatively connected to a plurality of acoustic transceivers; wherein a first acoustic transceiver of the plurality of acoustic transceivers is operatively connected to a first multi element transducer array mounted on an aquatic sensor platform and operated at a first acoustic frequency; and wherein a second acoustic transceiver of the plurality of acoustic transceivers is operatively connected to a second group of at least one transducer mounted on the aquatic sensor platform and operated at a second acoustic frequency different than the first acoustic frequency; characterized in that the digital circuit is configured to: receive a first analog signal from each transducer of the first group of at least one transducer; repeatedly sample the first analog signal with a periodic delay between repetitions, the periodic delay being an integer number of periods of the respective acoustic frequency of the respective acoustic transceiver operatively connected to the respective transducer, wherein each sample constitutes a pair of values separated by one quarter of the period of the first acoustic frequency; receive a second analog signal from each transducer of the second group of at least one transducer; sample the second analog signal; process the pairs of values as components of Doppler velocity estimates, the members of the pairs representing the cosine and sine components of a Doppler-shift signal; and wherein the first acoustic transceiver is operatively connected to the first multi-element transducer array adapted to measure three dimensional motion within a first volume of the aquatic environment with at least four beams; wherein the second acoustic transceiver is operatively connected to the second group of at least one transducer adapted to measure range to an object within a volume of the aquatic environment angularly coincident with the first volume.