Chlorophyll-a (Chl-a) concentrations were measured at four sites around Unguja, Zanzibar during the northeast (NE) and southeast (SE) monsoon seasons. Data for Chl-a, nitrate, phosphate, ammonia, dissolved oxygen, sea sur face temperature, pH and salinity were collected once a month from March 2008 to March 2009. The SE monsoon had insignificantly higher Chl-a compared to the NE monsoon season when Chl-a for Bawe, Chumbe, Pongwe and Mnemba were combined (W = 234, p = 0.93). The drivers of high Chl-a during the SE monsoon were ammonia and nitrate. Results from individual sites showed that Pongwe and Mnemba had higher median Chl-a during the SE than the NE monsoon season. Temperature, dissolved oxygen and ammonia were the major factors that influenced high Chl-a at these sites. In contrast, Chumbe and Bawe had higher median Chl-a during the NE- than the SE mon soon season. The major factors influencing high Chl-a in the NE at Chumbe and Bawe were high levels of nutrients, mainly from sewage effluent and various human activities around the coast in Zanzibar town. The interaction of Chl-a between monsoon seasons (NE and SE) and sites (Bawe, Chumbe, Pongwe and Mnemba) was insignificant (F(1,3) = 1.3144, p = 0.2949). The principal component analysis revealed that different physical and chemical environmental variables affect Chl-a concentration over time and location.Funded by the Global Environment Facility (GEF) for the financial support of this work through the Coral Reef Targeted Research and Capacity Building for Management (CRTR) project to the University of Dar es Salaam.