The relationships between chlorophyll-a (Chl-a), nutrients and other physico-chemical variables are important for marine water management strategies. In this study, monthly Chlorophyll-a (Chl-a) concentration, temperature, salinity, pH, dissolved oxygen and nutrients were measured at two sites (Bawe and Chwaka Bay) in Zanzibar coastal waters from May 2012 to May 2013. The mean Chl-a concentration ranged from 0.69 mg/m3 to 1.86 mg/m3, with insignificant variation between the sites, and significant differences among the stations being higher in near shore stations than in open seawater stations (t= 5.296, P < 0.0001). The results revealed significant higher Chl-a concentration during the southeast monsoon (SEM) than the northeast monsoon (NEM) (t = 2.871, P < 0.0152). In addition, the results showed that, the concentration was significantly correlated positively with salinity (r = 0.640; p = 0.019) and negatively with NO3 (r = -0.563; p = 0.044). The results of this study suggest that high Chl-a concentration to the near shore station is due to sewage system which influence nutrients concentrations, hence result into high Chl-a concentration. Furthermore, the SEM experienced high Chl-a concentration due to strong winds which bring nutrients to the sea surface which favour growth of phytoplankton hence result into high concentration.Funded by the Carnegie Corporation of New York through a grant to the University of Dar es Salaam, Institute of Marine Sciences, via the WIORISE Project.