Fouling of spiral-wound reverse osmosis (SWRO) membrane systems is a pervasive problem. Here we demonstrate that a mobile, low cost magnetic resonance imaging (MRI) apparatus operating at the earth’s magnetic field (low magnetic field, LF) can non-invasively (i) image the inside of a SWRO membrane system with glass fiber outside casing in a pressure vessel during cross flow operation and can (ii) detect the location of foulant, in this study sodium alginate. LF-MRI images of the module were successfully acquired in less than eight minutes using a spin-echo protocol, the internal structure of the modules was clearly evident and images compared well with high resolution MRIs obtained using a large-sized, costly high magnetic field superconducting MRI system. By parameter optimisation (specifically the echo time employed) it was possible to differentiate flowing and stagnant fluid in the clean and fouled membrane systems, and to determine the presence of alginate foulant on the feed-side of the fouled SWRO membrane system. This study motivates further investigation of the sensitivity of LF-MRI and the development of bespoke low cost LF-MRI hardware for the monitoring of industrial SWRO membrane installations.