Scale formation of sparingly soluble salts has a significant effect on flux decline in nanofiltration (NF) system. This study focuses on the elucidation of the different mechanisms of scale formation according to membrane modules in NF system. In unstirred batch NF, flux decline was mainly due to surface (heterogeneous) crystallization, while in crossflow NF, fouling was attributed to both surface and bulk crystallization. However, the extent of contribution of each crystallization to the fouling depended on the NF modules. The bulk (homogeneous) crystallization followed by crystal deposition on the surface of the nanofilter played a major role in flux decline in the spiral wound module whereas surface blockage due to the surface crystallization does in the tubular module. When an on-line microfiler was introduced to prevent crystal deposition during the concentration run, flux improvement was pronounced only in case of the spiral wound module, whereas it was negligible in case of the tubular module. This was because the microfilter could only remove crystals formed in the retentate through the bulk crystallization which is the dominant fouling mechanism in the spiral wound module. A modified resistance-in-series model was applied to assess the fouling characteristics of each NF module based on the bulk and the surface crystallization. The greatest extent of the fouling due to surface crystallization in tubular module was attributed to its highest concentration polarization modulus compared with the other two modules at the same crossflow rate.