Early diagenetic processes in hemipelagic sediments of the Panama Basin (∼3900 m) are strongly influenced by an active benthic community and intense bioturbation comparable to organic-rich, shallow water deposits. Rapid reworking enhances the role of suboxic decomposition, particularly Mn cycling, and burrow formation increases biogeochemical heterogeneity as reflected in pore-water profiles. Apparent regular patterns in the distribution of some solutes, such as NH +4 and Mn 2+, around identifiable burrow structures are consistent with the active irrigation of burrows and a biogenic origin for heterogeneity. The effects of infauna are sufficiently pervasive, relative to the size of normal samples, that similar variations in solute patterns between cores can be observed when samples are separated over wide-ranging spatial scales, from a few centimeters to hundreds of meters. The spatial variation in pore-water solute distributions in samples (cores, passive-equilibration "peepers") taken during a single cruise is comparable to the interannual variability observed between cruises over a 4 yr period. Mineralized tubes and associated burrow complexes are direct visual evidence for biogenic heterogeneity in these deposits and for a significant interaction between macroinfauna and suboxic microbial communities. Comparison of in situ peeper arrays with cores processed on board ship confirms a variety of retrieval and handling artifacts also inferred in other studies. These appear to be largely related to core warming, promoting lysis of biomass, dissolution of biogenic debris, and irreversibly producing subsurface NH +4 maxima and increasing concentration gradients of NO -3, NO -2, and Si(OH) 4. Agreements and mismatches between solute fluxes predicted from cores, in situ peeper arrays, and a benthic flux incubation chamber are consistent with various retrieval artifacts and with the enhancement of NO -3 (nitrification) and Si(OH) 4 fluxes by burrow irrigation. Unlike organic-poor, deep-sea deposits from oligotrophic regions, where the sediment-water interface can be the site of most benthic decomposition, subsurface processes are significant in the Panama Basin, and average reaction rate attenuation with sediment depth, is similar to that in bioturbated shallow-water deposits.