Fungal biogeochemical activity over a long-term scale may have negative environmental consequences for the management of barrier materials used in nuclear waste disposal. Fungal deterioration of barrier concrete was studied in microcosms simulating a heterogeneous environment with an external source of nutrients for the fungi. Fungi successfully colonized barrier concrete, generally avoiding granite aggregates, and biochemically (by excretion of protons and ligands) and biomechanically deteriorated the concrete. Fungi dissolved the cement matrix leaching structural elements and accumulating them within the fungal biofilm and associated microenvironment. Oxalate-excreting Aspergillus niger formed abundant calcium oxalate crystals on the concrete and encrusting fungal hyphae.