The physical controls on salt distribution and river-sourced conservative solutes, including the potential implications of climate change, are investigated referring to model simulations of a macrotidal estuary. In the UK, such estuaries typically react rapidly to rainfall events and, as such, are often in a state of non-equilibrium in terms of solute transport; hence are particularly sensitive to climate extremes. Sea levels are projected to rise over the 21st century, extending the salinity maximum upstream in estuaries, which will also affect downstream solute transport, promoting estuarine trapping and reducing offshore dispersal of material. Predicted ‘drier summers’ and ‘wetter winters’ in the UK will influence solute transport further still; we found that projected river flow climate changes were more influential than sea-level rise, especially for low flow conditions. Our simulations show that projected climate change for the UK is likely to increase variability in estuarine solute transport and, specifically, increase the likelihood of estuarine trapping during summer, mainly due to drier weather conditions. Future changes in solute transport were less certain during winter, since increased river flow will to some extent counter-act the effects of sea-level rise. Our results have important implications for non-conservative nutrient transport, water quality, coastal management and ecosystem resilience.