The introduction of a deuterium-enriched tracer to benthic incubation chambers emplaced on the sea floor of Port Phillip Bay provides a method of modelling bio-irrigation within the sediments. Plots of deuterium v. incubation time reveal that all seven chambers, emplaced at four sites, indicate nondiffusive transport of pore-water solutes across the sediment-water interface. Modelling indicates that advection of overlying chamber water must occur to depths of 20-50 cm below the interface and at rates between 150 and 700 mL h-1. Multiple chambers deployed in the same region within the bay are consistent with respect to bio-irrigation depth and rate. This indicates that the distribution of infauna responsible for irrigation is quite consistent within regions defined by sediment type and depth. However, various regions in the bay show distinctly different irrigation rates; thus the distribution and/or activity of infauna is not constant throughout the bay. At the lower rate of pore-water advection, the entire water column in Port Phillip Bay passes through the sediments within 200 days. Dissolved caesium, injected into the chamber, is also an effective tracer of bio-irrigation although adsorption onto sediment particles increases the uncertainty of model results.