Phytoplankton primary production and copepod production, and the size composition of the phytoplankton community in Tolo Harbour, a semi-enclosed bay in north-eastern Hong Kong, were studied from February 2008 to March 2009. Chlorophyll-a (Chl a) concentrations decreased from an average of 9.07 µg l−1 in the inner part of the bay to 3.07 µg l−1 at the mouth of the bay. In terms of contribution to total Chl a biomass, the >20 µm size fraction dominated the phytoplankton community. The zooplankton community in Tolo Harbour was dominated by small copepods, with cephalothorax length ranging from ~0.3 to 0.4 mm, and the density of copepods decreased from ~15,000 ind.m−3 in the inner part of the bay to ~9,700 ind.m−3 at the mouth of the bay. Depth-integrated net primary production in Tolo Harbour was high, ranging from 0.34 to 10.40 g C m−2 day−1, with an overall mean of 2.64 g C m−2 day−1. In contrast, copepod production was low, ranging from 0.19 to 16.64 mg C m−3 day−1, with an overall mean of 2.73 mg C m−3 day−1. The low transfer efficiency of 1.4% between phytoplankton primary production and copepod secondary production suggests that the large phytoplankton was inefficiently grazed by the small copepods in Tolo Harbour.