Phytoplankton can indirectly indicate health status of coral reefs due to their sensitivity to changes in water quality parameters. This study explored the spatial and temporal variability in water quality and nutrients in relation to phytoplankton community composition and chlorophyll a concentration at Bawe, Mnemba, Chumbe and Pongwe coral reef sites in Unguja Island. In situ measurements of dissolved oxygen, temperature, salinity and pH were done every month for 1 year. Surface water samples were collected for determination of phytoplankton composition, nutrients and chlorophyll a concentration. Dissolved oxygen, temperature, salinity and pH did not differ significantly among the four sites (p > 0.05) but showed significant temporal variations among months (p < 0.05). Bawe had significantly higher phosphate concentration (1.45 ± 0.57 µg L−1) than Chumbe (0.74 ± 0.53 µg L−1), Mnemba (0.42 ± 0.30 µg L−1) and Pongwe (0.28 ± 0.10 µg L−1; p < 0.05). Similarly, Bawe had significantly higher nitrate concentration (0.81 ± 0.43 µg L−1) than Mnemba (0.33 ± 0.14 µg L−1) and Pongwe (0.24 ± 0.13 µg L−1; p < 0.05) but similar to Chumbe (0.90 ± 0.35 µg L−1; p > 0.05). However, values obtained at all the studied sites were less than 3 and 14 mg L−1 for phosphate and nitrate, respectively, for eutrophic oceans. Phytoplankton species were dominated by Bacillariophyceae (70.83 %) and some species identified such as Ceratium sp., Dinophysis sp., Protoperidinium sp., Prorocentrum sp., Oscillatoria sp. and Dictyocha fibula are known to produce toxins that affect fish species. Bawe had significantly higher chlorophyll a concentration (0.47 ± 0.07 mg L−1) than Mnemba (0.33 ± 0.04 mg L−1 ) and Chumbe (0.33 ± 0.04 mg L−1; p < 0.05). Chlorophyll a concentration was spatially inversely related to distance from Unguja town (p < 0.05) while it was temporally significantly positively correlated with dissolved oxygen, nitrate and phosphate (p < 0.05). The study revealed that, the coral reef sites have low nutrient levels and are in good health. The existence of toxic phytoplankton species suggests careful consumption of fisheries resources at the four coral reef sites and frequent monitoring for Harmful Algal Blooms (HABs) is required. The higher nutrients and chlorophyll a concentrations at Bawe Island compared to other sites calls for mechanisms to limit the release of domestic sewage from households and hotels to safeguard the coral reefs.