Scotland's marine food webs support a diversity of species and habitats. They contribute to maintaining the balance of the natural environment. Previous studies show that these ecosystems are contaminated by persistent organic pollutants and trace metals; with animals in higher trophic levels (e.g. cetaceans and pinnipeds) containing concentrations that are among the highest found in the ocean. Contaminants represent one of many pressures to which species and habitats are exposed. In assessing the contribution of contaminants to the overall pressure, measuring contaminants at a specific trophic level and then using trophic magnification factors (TMFs) to estimate concentrations at other trophic levels permits assessments across the food web, as well as allowing the adjustment of contaminant concentrations to a particular trophic level for comparison to assessment criteria. Fatty acid (FA) signatures and stable isotope (SI) ratios were used to develop a picture of Scottish marine food web ecology and reliably ascribe trophic levels to a wide range of species. Fatty acid trophic markers (FATMs) were used as trophic level indicators and with SI analysis, permitted identification of the mean trophic level of each species and determination of the feeding patterns and predator-prey relationships existing in the Scottish marine food web. Two hundred and eleven (211) samples comprising of seven fish species, one shark species, fourteen marine invertebrate species, three marine mammal species and two zooplankton species from different locations around Scotland were found to have mean trophic levels ranging from 1.47 ± 0.11 in zooplankton to 5.02 ± 0.35 in harbour seal. Fatty acid profile showed specific dietary information which differed between the eleven taxonomic classes and twenty-seven species. The organic and inorganic contaminant concentrations of the species for which trophic level has been determined, together with TMFs, will be reported in future papers.