We analysed the responses of Anabaena doliolum to elevated levels of copper and zinc in batch and semi-continuous cultures. Approximately 10, 4 and 8 and 5-times greater inhibition in final yield of A. doliolum occurred at 1, 2 μM Cu and 2.5 and 5 μM of Zn, respectively, in semi-continuous culture in comparison to batch culture. Protein, chlorophyl a and carotenoid contents of A. doliolum showed significantly (P<0.05) higher inhibition by test metals in semi-continuous culture than in batch culture. The greater sensitivity of different parameters of the test organism was related to the high metal content of the cells grown in semi-continuous system. Moreover, enhancement of pH of the culture suspension in batch culture showed a negative relationship with metal accumulation, and therefore with toxicity. This was due to decrease in free ionic concentrations of test metals. Carotenoids acted as a metal detoxifying agent by minimizing metal-induced inhibition in batch culture as was evident from its negative relationship with metal toxicity. © EDP Sciences, 2009.