The Fitzroy impoundment is a long slender water body (10 m deep) formed by the regulation of the Fitzroy River in tropical Australia. Large, monsoonally driven discharges in late summer flush the impoundment repeatedly leaving, after 2 months, a longitudinally uniform, well-mixed water column, rich in dissolved nutrients and with high turbidity. For the rest of the year flows are negligible. Paradoxically, two sites with initially identical nutrient and stratification characteristics, and located only 30 km apart, develop quite different patterns of cyanobacterial succession. The upstream site is initially dominated by Anabaena circinalis which appears in early spring and collapses within the month. A mixed population of Anabaenopsis elenkinii and Aphanizomenon issatschenkoi then develops at both sites. This is followed by a mixture of small cyanobacteria (consisting of Cylindrospermopsis, Planktolyngbya and Limnothrix) which develops mainly at the downstream site and persists for 3 months until flushed away by flood flows. We report on data covering an 8 month period of investigation of the stratification, light climate, temperature and nutrient dynamics at these two sites. We show that large-scale climatic conditions and the local weather pattern set the physical and chemical conditions which determine the cyanobacterial response.