Abstract An investigation about the in vivo inactivation of photosynthetic water oxidation has been carried out in the cyanobacterium Anacystis nidulans (Synechococcus PCC 6301). Photosystem II and photosystem I activity as well as the relative amount of the D1 and manganese stabilizing peptide of photosystem II were determined after growing the cells in nutrient media with variations in the nitrogen source and the concentration of the major divalent cations (Mg2+ and Ca2+). The results show a rapid inactivation of water oxidation in A. nidulans in response to nitrogen deficiency and in response to reduced Mg2+ and Ca2+ concentrations. The inactivation of water oxidation observed under divalent cation deficiency could be greatly accelerated when L-amino acids instead of ammonia or nitrate were used as nitrogen source. Under these conditions inactivation of water oxidation correlated with a rapid loss of D1 and with a slower loss of the manganese stabilizing peptide from photosystem II. A possible regulation of the photosystem II activity in A. nidulans by nitrogen metabolites is suggested.