This study aimed to gain a better understanding of the metabolic fate of dietary fatty acids in rainbow trout, with a specific focus on the effect of varying total C18 PUFA level. Fish were fed a control fish oil based diet or one of five experimental fish oil deprived diets formulated with a constant 1/1 ratio of 18:3n-3/18:2n-6 and varying total C18 PUFA levels for a period of 7 weeks. The transcriptional changes of the Δ-6 desaturase and elongase enzymes in direct comparison to in vivo fatty acid bioconversion, estimated using the whole-body fatty acid balance method, were analysed. The main findings were that i) the efficiency of Δ-6 desaturase was negatively affected by C18 PUFA availability, but the total apparent in vivo enzyme activity was directly proportional to C18 PUFA substrate availability; ii) Δ-6 desaturase had a greater affinity towards n-3PUFA than n-6PUFA; iii) excessive C18 PUFA substrate availability could limit the availability of Δ-6 desaturase to act on C24 fatty acid; iv) the elimination of dietary n-3LC-PUFA (enzyme products) up-regulated the transcription rate of Δ-6 desaturase; but v) the total apparent in vivo enzyme activity was directly and positively affected by substrate availability, and not product presence/absence nor the extent of the enzyme transcription rate.