This chapter addresses the biological processes that influence community composition and dynamics, highlighting the multi-trophic and multi-functional nature of soft-sediment communities. Characterising the biological interactions into competition, predation, adult–juvenile interaction, facilitation, parasitism and disease, the chapter initially focusses on what we know about these processes, their effect on other biological components and their importance in different benthic habitats. It then extends to consider how they, in conjunction with mobility of species, can influence the broader-scale spatial structure and temporal dynamics connecting communities and functions. The chapter recognises the importance of differences in strength of interaction and the potential for weak interactions to affect community dynamics. This is framed around the concept of self-organisation as an emergent characteristic of ecosystem interaction networks and how meta-communities may be constructed.