Competitive interactions between marine mammals and fisheries represent some of the most complex challenges in marine resource management worldwide. The development of commercial fisheries and recovering marine mammal populations have contributed to a decrease in fish availability. Whilst ecosystem-based fisheries management (EBFM) can counteract this decrease, achieving the EBFM objectives faces certain major obstacles including insufficient or unreliable data, inapplicable assessment models, as well as inadequate management decisions that do not account for fisheries-induced morphological alterations (FIMA) and marine mammal management. Despite a body of evidence addressing various aspects of marine mammal-fisheries competition, little is known about the effects of marine mammal-fisheries biological interactions affecting the fish viability and food web stability. We review the research on marine mammal-fisheries competitive biological interactions (hereafter biological competition) by focussing on (1) the prerequisites for marine mammal-fisheries biological competition and the relevant methodologies to explore them and (2) recent studies revealing the implications of FIMA and trophic interactions for the biological competition. We also discuss the implications of FIMA, eco-evolutionary feedback and prey-predator dynamics for EBFM implementation in contemporary harvested ecosystems. Our main findings reveal a lack of data about marine mammals’ prey choice and selectivity, the need for better representation of marine mammals in modelling approaches and lastly, the necessity for additional research linking FIMA, trophic interactions and the EBFM objectives. To conclude, interdisciplinary approaches may serve to link all of the efforts needed to effectively and holistically support the implementation of EBFM.