Traditionally, trophic ecology research on aquatic ecosystems has focused more on the quantity of dietary energy flow within food webs rather than food quality and its effects on organisms at various trophic levels. Recent studies emphasize that food quality is central to consumer growth and reproduction, and the importance of food quality for aquatic ecosystems has become increasingly well recognized. It is timely to synthesise these findings and identify potential future research directions. We conducted a systematic review of omega-3 polyunsaturated fatty acids (ω3-PUFAs) as a crucial component of high-quality food sources in freshwater ecosystems to evaluate their impact on a variety of consumers, and explore the effects of global change on these high-quality food sources and their transfer to higher trophic consumers within and across ecosystems. In freshwater ecosystems, algae rich in ω3 long-chain PUFAs, such as diatoms, dinoflagellates and cryptophytes, represent important high-quality food sources for consumers, whereas cyanobacteria, green algae, terrestrial vascular plants and macrophytes low in ω3 long-chain PUFAs are low-quality food sources. High-quality ω3-PUFA-containing food sources usually lead to increased growth and reproduction of aquatic consumers, e.g. benthic invertebrates, zooplankton and fish, and also provide ω3 long-chain PUFAs to riparian terrestrial consumers via emergent aquatic insects. Consumers feeding on high-quality ω3-PUFA-containing foods in turn represent high-quality food for their own predators. However, the ω3-PUFA content of food sources is sensitive to global environmental changes. Warming, eutrophication, increased light intensity (e.g. from loss of riparian shading), and pollutants potentially inhibit the synthesis of algal ω3-PUFAs while at the same time promoting the growth of lower-quality foods, such as cyanobacteria and green algae. These factors combined could lead to a significant reduction in the availability of ω3-PUFAs for consumers and constrain their overall fitness. Although the effect of individual environmental factors on high-quality ω3-PUFA-containing food sources has been investigated, multiple environmental factors (e.g. climate change, human activities, pollution) will act in combination and any synergistic effects on aquatic food webs remain unclear. Identifying the sources and fate of ω3-PUFAs within and across ecosystems could represent an important approach to understand the impact of multiple environmental factors on trophic relationships and the implications for populations of freshwater and riparian consumers. Maintaining the availability of high-quality ω3-PUFA-containing food sources may also be key to mitigating freshwater biodiversity loss due to global change.