Globally, there is an increasing trade-off between efforts to attain human water security and minimise ecosystem threats. Poorly planned efforts to meet current human water demands may jeopardise the ecological integrity of the river basins and may put future water security at risk. This article assesses the trade-offs between the future human and ecosystem water security threats in the South East Queensland Region, Australia. The article evaluates future water security threats based on a set of water and ecosystem services-related indicators and an ensemble of all climate change scenarios and models on water flow. It predicts the hotspots with higher human water security and ecosystem threats in 2040. The article finds that 52.1 per cent of the region may be affected in 2040 with either higher human water security risk or ecosystem services risk and, in some cases, with both. The challenge of managing the trade-offs is complex in regions with higher economic activities, which cover 16.3 per cent of the region. The research recommends that mitigation measures that address human water provision and nature conservation will need to be balanced and put at the same level of importance in these regions that are more affected.