Changes in the hydraulic properties of porous material due to bioclogging have been observed in many laboratory simulations and field studies. Because such changes in hydraulic properties influence the movement of fluids and contaminants, microbial ecology data are required for improved transport modeling. Here we investigate the effects of environmental variables previously shown to influence bioclogging, specifically oxygen availability, sediment grain size, and organic carbon (nutrient) concentration on the hydraulic properties of simulated subsurface environments. Our study provides evidence of a different clogging mechanism for aerobic and anaerobic microbial communities under high organic carbon concentrations (400 mg L(-1)). This work also suggests that the clogging mechanism operating in anaerobic microbial communities is more sensitive to carbon availability than that in the aerobic microbial communities. We found that grain size does have an effect on clogging, but it appears that there is a threshold carbon concentration, and therefore biomass, below which these effects are insignificant. Differences between the microbial communities that developed under different oxygenation conditions were detected using 16s rRNA analysis.