A novel magnetic resonance measurement (MRM) protocol for non-invasive monitoring of fouling in spiral wound reverse osmosis (SWRO) membrane modules is demonstrated. Sodium alginate was used to progressively foul a commercial SWRO membrane at industrially relevant operating conditions in a circulating flow loop. The MRM protocol showcased the following: (i) earlier, more sensitive detection and quantification of fouling in the membrane module compared to feed-channel pressure drop. This was achieved using appropriate detection of the total nuclear magnetic resonance (NMR) signal. (ii) 2D cross-sectional imaging of the location of the accumulated foulant material; this was preferentially located adjacent to the membrane spacer sheet nodes, which was subsequently confirmed by a module autopsy. This image contrast, which could also readily differentiate the membrane, feed spacer and permeate spacer regions, was realised based on differences in the NMR relaxation parameter, T2,eff. (iii) High frequency acquisition of 2D cross-sectional velocity images of the module revealing very localised flow channelling in response to gradual foulant accumulation which impacted significantly on the flow pattern within the central permeate tube. Collectively this NMR/MRI measurement protocol provides a powerful analysis tool for the evolution of fouling in such complex modules, thus ultimately enabling more informed module design.