The phytoplankton community composition, abundance and size-fractionated biomass (chlorophyll a) along with various physical and chemical parameters were assessed in Kingston Harbour, Jamaica. Monthly sampling was conducted at 31 stations, each with two sampling depths throughout
the harbor between December 1993 and February 1995. The objectives of this study were to characterize the phytoplankton community of Kingston Harbour, to use this community structure to identify possible horizontal zonation and vertical stratification of the water mass in the harbor, and compare
this with previous findings. Results suggested that the water mass of the harbor shows temporary vertical stratification during the wet seasons into a less saline surface layer and a more saline deep layer as defined by significant differences in the mean total phytoplankton biomass and cell
abundance. Mean number of cells per liter in surface waters during the wet season ranged from 7 × 105 to 10 × 107 cells L−1 compared to lower values for deep water that ranged from 3 × 105 to 9.3 × 107 cells
L−1. Values for mean total biomass in surface waters during the wet season ranged from 1.01–24.5 mg chl a m−3, as compared to lower values in deeper water, which ranged from 0.56–22.1 mg chl a m−3. Determination of
stratification using the phytoplankton community was difficult to assess since most phytoplankton exhibit the tendency to sink through the water column while motile forms exhibit vertical migration between surface and deeper waters. Phytoplankton biomass was, however, very reliable for defining
horizontal zones across the harbor. This was true for both surface and deep waters at each station in the harbor. Total and size fractionated chlorophyll a in surface waters indicated three zones; one being the surface water layers of the upper basin and the inner harbor, the second
being the outer harbor, and the surface water layers of Hunts Bay formed the third zone. However, multiple range tests conducted on deep water chlorophyll a data defined four zones in the harbor: the deep water layers of the upper basin, the inner harbor, the outer harbor, and Hunts
Bay, respectively. Dissolved oxygen and NO3 − N + NO2 − N concentrations supported the horizontal zonation pattern defined by the phytoplankton community.
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