In this paper, the semi-enclosed bay named Tolo Harbour and Channel in Hong Kong, which was frequently attacked by red tides, was used as a case study. Data sets related to marine water quality, river nutrients, and meteorological conditions recorded between 1988 and 1999 were chosen for statistical analysis. A multivariate analysis showed that algal growth, represented by the chlorophyll a concentration, had obvious spatial and temporal variations in the study area. The chlorophyll a concentration had a consistently decreasing trend from the inner part of the Harbour and surface waters to the outer part and bottom waters. The temporal variations had a markedly seasonal variation with high bioproductivity in spring and winter. There were long-term fluctuations in the chlorophyll a concentration with a high-low-high pattern in the study period. Nutrients and hydrological and meteorological conditions were important factors of algal bloom. Besides nitrogen, which was the most critical factor of algal bloom for the whole water body, total phosphorus in the surface waters and phosphate (PO4) and silica (SiO2) in the bottom waters also showed strongly positive or negative correlations with the chlorophyll a level. For the meteorological conditions, global solar radiation was the key factor of massive algal bloom in the study period, while rainfall and wind direction were the most important factors of seasonal variation.