Macrofaunal activity in aquatic sediments can result in particle transport over short length scales, and can significantly modify the mechanical and hydraulic response of aquatic sediments to imposed stresses. A simple approach to characterizing biological effects on sediment stability is to consider three forms of biota/sediment interactions: structural/stratigraphic, which includes constructional modifications of and particle transport within the seabed on scales much larger than sedimentary particles or aggregates; rheological, including biogenic modification of sediment strength; and particulate, which includes finer-scale effects related to modifications of effective particle size. Each class of biogenic influence can occur in most aquatic environments and exert unique influences toward facilitating or hindering the initiation of sediment transport, as well as redistribution of sediments and particle-borne contaminants through the seabed. The relative importance of these processes with respect to initiation of sediment transport diminishes with increasing excess hydrodynamic shear stress. However, for cases where contaminants are associated with fine, cohesive sediments, and hydrodynamic conditions are only episodically intense, these factors become more significant in terms of contaminant fate and transport. Although these biogenic influences on sediment properties have been recognized for several decades, their effects are not generally incorporated into quantitative models for sediment and contaminant fate/ transport. In this paper, we will look at examples of such biogenic influences, and consider approaches for quantifying and modeling these effects on sediment stability.