Carbon (δ(13) C) and nitrogen (δ(15) N) analysis has been extensively used to investigate the importance of marine foods in the diet of archaeological populations in the North Atlantic Islands; however, few faunal studies exist to aid the interpretation of results. Palaeoenvironmental modelling of δ(13) C and δ(15) N values is crucial in determining whether changes in the stable isotope values are a result of dietary change, rather than temporal or geographical fluctuations in carbon and nitrogen. Investigating faunal dietary behaviour can provide an insight into past foddering and land management strategies. Detailed sampling of wild and domestic species for bulk collagen analysis was undertaken in order to characterise geographical variations in δ(13) C and δ(15) N values in the Outer Hebrides and Orkney. Samples from the Neolithic to the Norse period were analysed to assess temporal and geographical variations in δ(13) C and δ(15) N values, in addition to determining the contribution of marine foods to the diet of local fauna. A δ(15) N shift of 1‰ was observed between the Outer Hebrides and Orkney in the Neolithic and Iron Age. A geographical variation in δ(13) C values was observed in the Norse period between Orkney and the Outer Hebrides. Temporal fluctuations in δ(13) C and δ(15) N values demonstrate variations in foddering practices of sheep in the Outer Hebrides. Pig specimens from the Outer Hebrides demonstrated evidence of marine food consumption in the Iron Age. Faunal dietary behaviour can act as a vital indicator of the importance of marine resources in the past. Characterisation of faunal δ(13) C and δ(15) N values geographically and temporally is crucial in our interpretation of human dietary behaviour.