The coastal waters of Hong Kong have been influenced by a number of anthropogenic factors, including cultural eutrophication, land reclamation and dredging. The effects of climatic variability on phytoplankton dynamics may be difficult to discern in coastal ecosystems due to the interaction of climatic variability with anthropogenic effects. In this study, the influence of the El Nino-Southern Oscillation (ENSO), Pacific Decadal Oscillation (PDO) and North Pacific Gyre Oscillation (NPGO) on phytoplankton dynamics in Hong Kong coastal waters was examined from 1986-2004. Weak correlations were found to exist between chlorophyll a concentration (Chl) and the multivariate ENSO index and PDO index. However, strong correlations were found to exist between the NPGO index and Chl. The NPGO has been proposed to influence Chl concentration in the North Pacific through its influence on upwelling and nutrient concentrations. In the coastal waters of Hong Kong, which are highly impacted by cultural eutrophication, we propose a different mechanism. The NPGO is locally forced by surface wind variability and we have found a strong negative correlation between NPGO and wind speed in Hong Kong. By destabilizing the water column, high wind speeds are detrimental to phytoplankton growth and therefore we hypothesize that the relationship between the NPGO and phytoplankton dynamics is as a result of wind speed variability. We have shown that large scale modes of climatic variability can be important in controlling phytoplankton dynamics even in ecosystems which are markedly influenced by a number of anthropogenic factors.