The zooplankton communities off the north east coast of Scotland, Wee Bankie sand-banks, were studied with traditional net samples and for the first time, for this area, with acoustic methods. A series of zooplankton samples were collected during June 2010 and March/June 2011 together with a set of physical parameters of the water column. Taxonomic analysis of the collected samples enabled the characterisation of zooplankton communities. Neritic communities with oceanic influence were found along the north east coast of Scotland and over the Wee Bankie with spatial variability associated with higher densities of zooplankton inshore. Temporal variability was associated with the expected succession of dominant copepods from spring to summer. An appropriate scattering model, Distorted Wave Born Approximation, was used to predict the target strength of the major zooplanktonic groups and so solve the forward problem to verify a plankton separation algorithm. The algorithm isolated weak scattering targets of zooplankton using three frequencies (38, 120 and 200 kHz) and was used to study the zooplankton spatial distribution during June 2008-2011 in relation to the physical characteristics of the water column. Model predicted target strength for the major zooplanktonic groups was sensitive to orientation for large organisms and material properties for both copepods and euphausiids. The Wee Bankie waters were thermally stratified, with June 2011 the least stratified of all years. Depths of observed maximum backscatter varied in relation to the pycnocline depth and tended to be deeper in offshore stations. The estimated biomass from the observed backscatter increased from 2008 to 2011 but spatial patterns varied from year to year. Although, estimated biomass across years reduced with increasing maximum fluorescence and surface to bottom temperature difference, the same relationship was not evident within year.