Food web structure is the underlying framework of ecological communities and human systems and it is closely related to ecosystem resilience. Our ability to predict food web changes in response to anthropogenic stress is dependent on our understanding of the interactions among food web-stabilizing mechanisms, making the study of these interactions a critical need for future research in aquatic sciences. This review discusses potential interactions among mechanisms implicated in maintaining aquatic food webs such as changes in functional diversity, compartmentalization, importance of weak interactions and slow energy channels, modification of resource subsidies, stoichiometry and habitat complexity. It outlines potential research directions in aquatic sciences and discusses implications of considering these pathways in management and conservation.