Cyanobacterial blooms are a worldwide phenomenon in both marine and freshwater ecosystems and are predicted to occur more frequently due to global climate change. However, our future water resources may also simultaneously suffer from other environmental threats such as elevated amounts of humic content and consequent increased water colour, a phenomenon called 'brownification'. In order to investigate the effects of temperature and water colour in combination, we performed a mesocosm experiment combining a 3 °C increase in temperature and a doubling in water colour. With this, we created a projected future scenario for our water resources, and we specifically focused on how these changes would affect cyanobacterial bloom formation and toxicity. We showed that despite total cyanobacterial biomass remaining unaffected, the abundance of one individual cyanobacterial species, Microcystis botrys, increased in response to the combination of elevated temperature and increased water colour. Furthermore, population fluctuations in M. botrys explained the majority of the variations in microcystin concentrations, suggesting that this species was responsible for the more than 300% higher microcystin concentrations in the future scenario treatment compared to the ambient scenario. Hence, it was not a change in cyanobacterial biomass, but rather a species-specific response that had the most profound impact on bloom toxicity. We argue that understanding such species-specific responses to multiple stressors is crucial for proper management decisions because toxic blooms can significantly affect both biodiversity and ecosystem functioning, as well as ecosystem services such as drinking water supply and recreation. © 2013 John Wiley & Sons Ltd.