1. Understanding the degree to which aquatic and terrestrial primary production fuel tropical aquatic food webs remains poorly understood, and quantifying the relative contributions of autochthonous and allochthonous inputs is methodologically challenging. Carbon and nitrogen stable isotope ratios (δ13C, δ15N) can provide valuable insights about contributions of terrestrial resources and trophic position respectively, but this approach has caveats when applied in typical complex natural food webs. 2. Here, we used a combination of C, N, and H (δ2H) stable isotope measurements and Bayesian mixing models to estimate the contribution of terrestrial (allochthonous) and aquatic (autochthonous) inputs to fish and invertebrate communities in the Congo River (and some tributaries). 3. Overall, our results show that we gained power to distinguish sources by using a multiple tracer approach and we were able to discriminate aquatic vs. terrestrial sources (esp. including hydrogen isotopes). Fish δ2H values were clearly correlated with their food preferences and revealed a high level of variation in the degree of allochthony in these tropical aquatic communities. 4. At the community level, it is clear that terrestrial C3 plants are an important source fueling the Congo River food web. However, in order to better constrain source contribution in these complex environments will require more robust constraints on stable isotope values of algal and methane-derived C sources.