Noninvasive ¹H‐nuclear magnetic resonance (NMR) imaging was used to investigate the diffusive properties of microbial mats in two dimensions. Pulsed field gradient NMR was used to acquire images of the H₂O diffusion coefficient, D_s, and multiecho imaging NMR was used to obtain images of the water density in two structurally different microbial mats sampled from Solar Lake (Egypt). We found a pronounced lateral and vertical variability of both water density and water diffusion coefficient, correlated with the laminated and heterogeneous distribution of microbial cells and exopolymers within the mats. The average water density varied from 0.5 to 0.9, whereas the average water diffusion coefficient ranged from 0.4 to 0.9 relative to the values obtained in the stagnant water above the mat samples. The apparent water diffusivities estimated from NMR imaging compared well to apparent O₂ diffusivities measured with a diffusivity microsensor. Analysis of measured O₂ concentration profiles with a diffusion‐reaction model showed that both the magnitude of calculated rates and the depth distribution of calculated O₂ consumption/production zones changed when the observed variations of diffusivity were taken into account. With NMR imaging, diffusivity can be determined at high spatial resolution, which can resolve inherent lateral and vertical heterogeneities found in most natural benthic systems.