The burrows of macrobenthos represent an important class of sedimentary microenvironments which significantly influence chemical, biological, and physical characteristics of a deposit. In intertidal regions, the time-dependent changes in composition during ebb-tide of water contained in burrows is a sensitive indicator of biogenic and abiogenic chemical reactions in burrow walls and adjacent sediment. Comparison of time series water samples taken from Onuphis jenneri (polychaete) and Upogebia affinis (crustacean) burrows in the same tidal flat demonstrate substantial differences in biogeochemical microenvironments despite the spatial proximity of the two species. Both types of burrows are influenced by the same general kinds of biogeochemical reactions but the relative intensity of these reactions differs in each case. Evidence for both heterotrophic and chemoautotrophic metabolic activity in each burrow type comes from the build-up or consumption patterns in burrow water of solutes such as NH4+, NO3, Mn++, l, HPO4, and HCO3. Burrow irrigation models and the stoichiometry of solute build-up imply that Upogebia burrows are sites of more intense nitrification-denitrification and microbial activity generally than are Onuphis tubes. Upogebia burrow water is also distinctly undersaturated with respect to carbonate minerals and has high numbers of bacteria relative to Onuphis. In addition to reaction rates, burrow geometry and the adsorption-diffusive permeability properties of the burrow wall also affect transient behavior of solutes. The organic burrow lining of Onuphis shows linear adsorption isotherms for positive, negative, and neutrally charged solutes represented by NH4, HP04, and Si(OH)4. Diffusion-reaction modeling demonstrates that adsorption, in particular, can significantly lower the transient state concentrations of burrow water trace solutes even for tube wall thicknesses of only 200 μm. The observed differences between burrow microenvironments of the two species living in close proximity suggest distinct biogeochemical associations between microbes and species specific biogenic structures.