Zooplanktons are marine animal members of the planktonic community. They play a key role in marine ecosystem, by linking primary production to higher trophic levels. The spatial and temporal dynamics of zooplankton communities were studied in 4 station along a transect offshore of Doha Bay, Qatar, from June 2014 to March 2015. Zooplankton samples were collected by means of horizontal tows using 120 and 500μm mesh size plankton nets. Two methods of examination were used and intercalibrated: optical microscopy and the automated identification and counting equipment FlowCAM. No spatial variability was observed among the locations sampled, while temporal variability was detected. The faunistic groups contributing most to these temporal variations were Cladocera, Oikopleura, crab larvae, Lucifer typus, fish eggs, and jellyfish. Our results showed no significant differences between the use of either the automated (FlowCAM) or the optical identification and counting suggesting the possible use of both methodologies as they provide complementary information (accurate identification capabilities and size spectra or population structure data).