Stable isotope ratios (SIR) are widely used to estimate food-web trophic levels (TLs). We built systems dynamic N-biomass-based models of different levels of complexity, containing explicit descriptions of isotope fractionation and of trophic level. The values of δ15N and TLs, as independent and emergent properties, were used to test the potential for the SIR of nutrients, primary producers, consumers, and detritus to align with food-web TLs. Our analysis shows that there is no universal relationship between TL and δ15N that permits a robust prognostic tool for configuration of food webs even if all system components can be reliably analysed. The predictive capability is confounded by prior dietary preference, intra-guild predation and recycling of biomass through detritus. These matters affect the dynamics of both the TLs and SIR. While SIR data alone have poor explanatory power, they would be valuable for validating the construction and functioning of dynamic models. This requires construction of coupled system dynamic models that describe bulk elemental distribution with an explicit description of isotope discriminations within and amongst functional groups and nutrient pools, as used here. Only adequately configured models would be able to explain both the bulk elemental distributions and the SIR data. Such an approach would provide a powerful test of the whole model, integrating changing abiotic and biotic events across time and space.