A large number of studies across many different disciplines have been conducted on the Swartvlei estuarine system over the past five decades, thus providing an ideal opportunity to review spatial and temporal aspects of fish food webs in the lower estuary and upper lake. The aquatic and semi-aquatic macrophytes, together with the physico-chemical environment associated with these two parts of the system are very different, thus providing an immediate contrast in terms of habitat functioning for the associated fish assemblages. In addition, major macrophyte senescence is known to occur episodically in Swartvlei Lake, bringing with it major consequences for the trophic functioning of that part of the system. The scientific information on the Swartvlei estuarine lake system is reviewed and conceptual trophic diagrams created that encapsulate both the spatial and temporal aspects described above. The next step in our understanding of the trophic functioning of the Swartvlei system is to undertake stable isotope analyses in both the lake and estuary. To prepare for such a step, the global literature on the use of stable isotopes in estuaries is reviewed and some of the findings, particularly in relation to fishes and food webs in different habitats, are highlighted. One of the conclusions reached by this review is that microalgae, whether epipsammic, epiphytic and/or planktonic, have been under-estimated relative to estuarine macrophytes in terms of their importance to the nutrition and productivity of fishes in estuaries. The central role of detritus and associated microorganisms in providing trophic stability for invertebrates and fishes in estuaries is also highlighted. Finally, it is apparent that fishes do not rely on a single source of organic matter for growth and development, e.g. most carnivorous fish species rely on mixes of prey that use different organic sources for production, and that benthic/demersal fishes in particular seem to access food chains from different parts of the water column.