Contaminated aquatic sediments pose health risks to fish, wildlife, and humans and can limit recreational and economic uses of surface waters. Technical and cost effective in situ approaches for sediment management and remediation have been identified as a research need. Subaqueous in situ capping is a promising remedial approach; however, little is known regarding its impact on underlying sedimentary processes and the feasibility of bioaugmented caps at sites subject to contaminated groundwater seepage. This work specifically addresses (1) the impact of capping on biogeochemical processes at the sediment-water interface, (2) the ability and degree to which indigenous sediment microorganisms colonize an overlying cap, (3) the effect of advective flow direction on redox conditions within a cap, (4) natural contaminant bioattenuation processes within capped sediment, and (5) limitations toward a functional bioreactive in situ cap. Laboratory-scale experiments with capped sediment columns demonstrated that emplacement of a sand-based in situ cap induced an upward, vertical shift of terminal electron accepting processes into the overlying cap while simultaneously conserving redox stratification. Upflow conditions simulating a groundwater seep compressed anaerobic processes towards the cap-water interface. Microorganisms indigenous to the underlying sediment colonized cap material and spatial population differences generally reflected redox stratification. Downflow of oxic surface water through the cap, simulating tidally-induced recharge, created fully oxic conditions within the cap, demonstrating that flow direction strongly contributes to redox conditions. Experiments simulating capped sediment subject to contaminated groundwater seepage revealed a reduction of natural bioattenuation processes with time, stemming from the elimination of labile organic matter deposition to the sediment and a subsequent lack of electron donor. Thus, parent contaminants within groundwater seeps will be subject to minimal biotransformations within the sediment before entering a reducing cap. A bioreactive cap, inoculated with microorganisms capable of reductive dehalogenation, was established to reductively dechlorinate tetrachloroethene present in the groundwater; however electron donor amendments to sediment effluent were required to achieve complete dechlorination of tetrachloroethene to non-toxic ethene. Results from this work improve understanding of biogeochemical and bioattenuation processes within capped aquatic sediments and should aid in the development of active capping technologies.