Low field Nuclear Magnetic Resonance was used to evaluate the effect of salt and modified atmosphere packaging (MAP) on cod loins during superchilled storage. Transversal and longitudinal proton relaxation times of the cod loins were measured with Carr–Purcell–Meiboom–Gill (CPMG) and Inversion Recovery (IR) pulse sequences respectively. The relaxation parameters reflected the observed differences in the muscle caused by variation in salt concentration, the choice of salting method (brining or brine injection) and packaging (air or MAP), as well as superchilled storage temperature and storage time. Significant correlations were found between the NMR parameters and parameters describing the water dynamics of the muscle (moisture and salt content, water holding capacity, drip and cooking yield), as well as muscle pH and counts of H2S-producing bacteria in chosen sample groups. The study showed the possibility of using low field NMR to indicate fish quality deterioration, when the spoilage mechanisms affect the water properties and muscle structure.