Estuarine areas are sites of human pressures and degradation. In order to maintain and/or restore the quality of estuarine ecosystems, it is necessary to describe their structure and functioning. For that reason, many recent scientific works focus on food webs, which are depicted as being good indicators of the functioning of aquatic ecosystems. Hence it is necessary to question how estuarine food webs can be described. This paper proposes a pragmatic and practical review of the most widely used techniques (stomach/gut content analysis, stable isotope ratios and biochemical markers) with emphasis on their main advantages, drawbacks and bias according to possible ecological goals (ecological quality objectives). These approaches, although quite different, provide complementary information about the trophic relationships in the system, that is to say the sources of organic matter and the description of energy flows between the different compartments of the food web. In trophic models, all these results can be integrated to a global picture of the estuarine trophic structure. This is considered to be an essential step towards the understanding of the functioning of these ecosystems.