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Biofilms, and collections of embedded microbial communities, present structural heterogeneities with functional consequences for important processes, such as transport. The origin of such structures has been unclear. Here, we propose that they can arise as a consequence of diffusive transport limitation. To illustrate, a model allowing internal heterogeneity is developed. Linear analysis is applied to a simplified version of the model suggesting that heterogeneity forms on (or below) the active layer length, a length scale that may not be suitable for homogenization, with non-trivial implications for system scale properties such as reduction in system-wide diffusive transport efficiency. Numerics suggest that the simplified model provides useful insight into behaviour of the full model. We then show examples based on microcolony formation in host domains and argue that internal heterogeneity can be related to community function.