Transport models in sediments commonly assume that diffusion occurs through water saturated pore space and that diffusive properties are largely homogeneous and isotropic. The bioturbated zone of marine sediments is characterized by sediment pores filled with mucus gel and criss-crossed by organic membranes that line macrofaunal tubes and burrows. Diffusion experiments utilizing pedal mucus from the naticid snails, Neverita (=Polinices) duplicata and Euspira (=Lunatia) heros, and organic tube linings from the polychaetes Onuphis jenneri, Diopatra cupria, and Chaetopterus variopedatus, demonstrated that the diffusion of both organic and inorganic solutes is inhibited by these common biogenic components. Diffusion of porewater DOC and Br tracer through mucus is reduced by factors typically 3–8X relative to free solution. Diffusion rates of DOC and Br through mucus and tube linings demonstrate that both charge and size inhibition commonly occur, however, charge discrimination was not observed for a range of inorganic solutes within mucus cements formed by the polychaete Melinna cristata. Diffusion of polystyrene sulphonates having varied molecular weights shows that inhibition of diffusion by mucus gel increases regularly with molecular size. No size exclusion or cutoff was observed up to molecular weights of at least 100 kDa. Although increases of solution viscosity by mucus (up to ∼ 170 mpoise), could explain solute diffusion inhibition to some extent, size and charge inhibition patterns imply that both mucus and tube linings behave as polyelectrolyte, fibrous meshworks with species specific properties (e.g. open channel patterns) rather than as polyelectrolyte solutions per se. The measured diffusion rates of bulk porewater DOC (0.387 cm2 d−1, 5°C) and of specific polystyrene sulphonates in sea water are substantially higher than predicted by extrapolation from measurements in distilled water, presumably as a result of ionic strength effects on molecular conformations. The transport of solutes, particularly DOC, in the bioturbated zone is greatly complicated by the presence of semipermeable mucus secretions and tube linings. Differential inhibition by biogenic secretions of the transport of specific classes of organic molecules such as exoenzymes, may be especially important to understanding faunal adaptations, processes governing the remineralization of organic matter, and linkages between macrofauna and microbial activities.