A finite element algorithm is presented to simulate fully coupled transient fluid flow, heat, and solute transport in discretely fractured porous media, and yield the regional-scale free thermohaline convection patterns for the McArthur Basin in northern Australia. Numerical results indicate that salinity variation throughout the basin has an important influence on fluid migration and the thermal regime. The spatial and temporal distribution of saline fluids can either promote or impede free convection. Relatively saline conditions (10 wt.%) at the basin floor favour free convection; whereas, high salinities at depth suppress the development of convective hydrothermal systems. When salinity increases with depth, a higher geothermal gradient is required to induce and maintain significant fluid circulation. The implication is that sedimentary-exhalative ore deposits are more easily formed when evaporation first produces surface brines, and then these brines sink and displace pore waters in the basin.