Experimental studies of the deposit-feeders Heteromastus flliformis, Tellina texana, and Macoma balthica demonstrate that, at natural population abundances, each species has major effects on sediment overlying water solute transport, bulk sediment reaction rates, and microbial distributions. Using Cl as a conservative tracer, one-dimensional transport models show that the effective diffusion coefficient, De, in the presence of these macrofauna is ∼2–5× the molecular diffusion value in the upper 8–12 cm of sediment. In general, the exact value of De is time dependent as shown by time-course experiments with Heteromastus and by comparison of one-dimensional model predictions with a transient-state, two-dimensional cylindrical coordinate model. This latter model takes into account changes in diffusion geometry caused by irrigated burrow structures. The magnitude of apparent time variation in De depends on burrow abundance, size, and depth of burrowing; larger values of De are measured at longer times of tracer transport. In contrast, the simple nonlocal parameter required to mimic the two-dimensional model distributions is essentially constant with time and can be related to different solutes by the ratio of their diffusion coefficients.Models of pore water distributions demonstrate that the production rates of NH4+ in sediments are increased by at least 20–30% in the presence of macrofauna compared to controls or anoxic incubations, regardless of the model used. This is presumably due to the overall lowering of inhibitory metabolite concentrations as well as stimulation of bacteria during grazing. Total bacterial numbers increase at depth in the presence of Heteromastus and Tellina relative to controls but are depleted in fecal material. A substantial increase in ATP/bacteria ratios occurs in fecal and surface sediment, presumably indicative of active growth and conversion from anaerobic to aerobic metabolism. Apparent elevated numbers and stimulation of metabolic activity is consistent with a "microbial gardening" effect by macrofauna.Most of the NH4+ produced in experimental sediment was apparently oxidized at the sediment-water interface and, along with the oxidation of sulfide and metals, results in a major surficial zone of low pH and HC03 consumption at a rate >24 meq/m2/d. This should cause substantial dissolution of CaCO3 as shown in previous studies. A zone of elevated Si(OH)4 production is also associated with the redoxcline, but Si(OH)4 is otherwise produced at a sufficiently slow rate that detectable decreases in concentration occur in irrigated sediments. Although no measurable effects of infauna on Si(OH)4 reaction constants could be demonstrated from pore water profiles, lowered concentrations result in higher net production rates, and sediment-water fluxes of Si(OH)4 increased in the presence of macrofauna by ∼1.4–1.6×, in agreement with theoretical models. Despite their limitations, the transport-reaction models and the two-dimensional or nonlocal parameterization models in particular, provide a consistent basis for description of the effects of macroinfauna on bulk sediment properties, and allow for comparison of different species at similar population abundances.