Numerical models of variable‐density groundwater flow and salt transport are a primary tool for predicting salinity distributions in coastal aquifers and estimating submarine groundwater discharge (SGD). Models are particularly useful to estimate the saline component of SGD, which can occur far offshore and is difficult to measure directly. Depending on the system and application, the level of geologic detail represented can range from homogeneous or layered to fully heterogeneous hydraulic conductivity fields. These features strongly affect model results, limiting understanding of subsurface salinity distributions and associated density‐driven saltwater circulation along coasts worldwide. In this study, the impact of the scale of representation of heterogeneity on salinity distributions and SGD was investigated using numerical simulations. Upscaling hydraulic conductivity can significantly modify salinity distributions and flow paths, resulting in unpredictable variations in simulated SGD, though the values for homogeneous fields with equivalent hydraulic conductivity show consistent trends. Simulated density distributions control both the rate and direction of subsurface saltwater circulation. The length of the mixing zone perimeter, a measure of salinity distribution complexity, is shown to correlate with both the rate of subsurface saltwater circulation and the amount of groundwater circulating in the reverse direction from homogeneous cases. Overall, the results demonstrate a strong dependence of salinity distributions and saltwater circulation on the scale and distribution of geologic heterogeneity represented in numerical models. This suggests that numerical models with simplified geologic structure may substantially underestimate saltwater circulation, and attempts to calibrate them using salinity distributions or SGD measurements may be problematic.