Fish bioaccumulate trace elements both from the surrounding water (across the gills) and through diet (via the gastrointestinal tract), with diet generally being the major contributor. A laboratory-based approach is currently the most appropriate way to precisely quantify the trophic transfer of trace elements in fish, and assimilation efficiency (AE) of trace elements from ingested food is a commonly determined parameter. However, there are still some discrepancies in the literature regarding the definition and the determination of AE in aquatic organisms and especially in fish. In this paper, we review the literature to provide a consolidated definition of the concept of AE as well as a description of the methods and protocols used to quantify the AE of trace elements. We also review the main studies of trace element AE in fish. Most studies reporting AE considered the effects of biotic factors, especially the influence of the quality of food, whereas abiotic factors have received less attention, although they affect fish physiology and, by extension, potentially affect the AE of trace elements. The need for further studies is thus noted, especially the influence of abiotic factors such as temperature, salinity or pH on trace element AE or in the context of the co-occurrence of multiple stressors; this will help us to better understand the trophic transfer of trace elements and thus their overall bioaccumulation in fish.