This project was conducted in the overall context of enhancing the natural salmon population of the River Allier and focused on growth performances of their juveniles and parr in a large temperate river. We focused on the development of juveniles Atlantic salmon released at fry stage into the wild and we integrated them in the context of the food chain. Our work had several objectives: (i) conduct a detailed analysis of diet, growth and nutritional status of parr raised in a salmon farm, released and recaptured along the continuum of the River Allier, (ii) assess whether, due to different fatty acid composition (FA), macroinvertebrates could affect parr growth and their overwintering survival, (iii) determine, through an approach based on FA biomarkers, the origins of lipid compounds found in macroinvertebrates and specify the sources of carbon assimilated by them along the river continuum. Sampling took place from June 2006 to October 2006 at monthly intervals. Samples of salmon, macroinvertebrates and different sources of organic matter were collected in five riffles along the river continuum (rhithron-epipotamon). Significant variations in growth, condition factor and lipid accumulation have been observed in restocked parr along the upstream-downstream gradient. The transition zone of rhithron-epipotamon appeared to be of great interest for salmon growth because of favourable environmental (temperature and flow) and trophic (preys composition and abundance) parameters. The values recorded in these areas were close to those achieved by the hatchery-reared salmon. In addition, growth performances seemed to result from dietary inputs of polar lipids (PL) from Baetids and Simuliids preferentially consumed by salmon in these downstream riffles. In contrast, the rhithron areas mainly located in trout zone, can be considered as the extreme upstream limit for 0+ salmon restocking. The low growth and lipid storage observed in this area appeared to result from lower dietary inputs in PL compared to the other riffles, not compensated by a significant input of neutral lipids from Chironomids. Thus, Simuliids and Baetids, preferentially consumed in downstream riffles, constituted an interesting type of food compared to Chironomids for parr overwintering survival and smoltification. The FA biomarkers approach showed that despite different feeding modes and whatever the localization of sites along the river continuum, macroinvertebrates consumed by parr receive their carbon from autochthonous production, more specifically on diatoms. A complementary approach by isotopic analysis of FA could confirm these origins of essential FAs in salmon and the relevance in the studied ecosystem of some FAs considered as biomarkers.