Saltwater intrusion is often occurring in coastal regions, and can substantially alter the chemical properties of groundwater. Thus, the micro-processes of mineral precipitation and the subsequent pore structure of porous media will evolve. However, these micro-processes have not yet been thoroughly studied. In this work, a series of column experiments were conducted to assess the evolution of ion exchange and simulate the mixing process of saltwater-freshwater that occurred in coastal aquifers after saltwater intrusion. The spatiotemporal distribution, morphological characteristics, and elemental composition of the precipitated minerals were characterized using nano-computed tomography, scanning electron microscopy, and energy dispersive spectroscopy mapping. The results revealed that mineral precipitation occurred throughout the columns. The number of smaller-diameter minerals with larger specific surface areas increased the most. The precipitated minerals contained mainly calcium and magnesium carbonates, and the morphology of the precipitated minerals varied, including block-, needle-, cube-, and rod-like precipitates. The mineral precipitates first filled the cracks in the quartz sand and then precipitated on the surface of quartz sand. Under the effects of ion exchange and mixing, quartz sand grains in the saltwater-freshwater mixing zone tended to become oversaturated and form precipitates. Moreover, the mineral precipitates preferentially nucleated rather than increasing in volume during the precipitation.