Magnetic resonance imaging (MRI) was used to spatially resolve the structure, water diffusion, and copper transport of a phototrophic biofilm and its fate. MRI was able to resolve considerable structural heterogeneity, ranging from classical laminations ϳ500 m thick to structures with no apparent ordering. Pulsed-field gradient (PFG) analysis spatially resolved water diffusion coefficients which exhibited relatively little or no attenuation (diffusion coefficients ranged from 1.7 ؋ 10 ؊9 m 2 s ؊1 to 2.2 ؋ 10 ؊9 m 2 s ؊1 ). The biofilm was then reacted with a 10-mg liter ؊1 Cu 2؉ solution, and transverse-parameter maps were used to spatially and temporally map copper immobilization within the biofilm. Significantly, a calibration protocol similar to that used in biomedical research successfully quantified copper concentrations throughout the biofilm. Variations in Cu concentrations were controlled by the biofilm structure. Copper immobilization was most rapid (ϳ5 mg Cu liter ؊1 h ؊1 ) over the first 20 to 30 h and then much slower for the remaining 60 h of the experiment. The transport of metal within the biofilm is controlled by both diffusion and immobilization. This was explored using a Bartlett and Gardner model which examined both diffusion and adsorption through a hypothetical film exhibiting properties similar to those of the phototrophic biofilm. Higher adsorption constants (K) resulted in longer lag times until the onset of immobilization at depth but higher actual adsorption rates. MRI and reaction transport models are versatile tools which can significantly improve our understanding of heavy metal immobilization in naturally occurring biofilms.The biofilm is an exceptionally common mode of life for bacteria in natural, clinical, and engineered environments. These microbial "cities" range in thickness from a few cells to several centimeters and display a complex three-dimensional architecture which exhibits both structural and compositional heterogeneity (10,22,23).Mass transfer rates within biofilms are controlled by diffusive and advective processes. Where interconnected pore spaces and channels exist within the biofilm, advection can play an important role in contaminant or nutrient mass transfer. In the cell clusters between channels or in biofilms where channels are absent, molecular diffusion becomes the dominant mass transfer mechanism (4, 21). Although the key transport medium within a biofilm is water, the molecular diffusion of a molecule through a biofilm is commonly slower than it is in free water due to the lower permeability of the biofilm and the tortuous nature of any pathways. Consequently, the diffusion of nutrients (or indeed contaminants) can be the rate-limiting step in biofilm performance and can lead to steep chemical and redox gradients through the community (4, 6, 9, 17, 23). For that reason, direct measurements of biofilm diffusion properties are highly desirable when modeling biofilm function (3,40). Biofilms, however, are complex structures which exhibit a high degree of stru...