The influence of small-scale differences in resource origin on trophic position estimates was evaluated with the stable isotopes method. Perch Perca fluviatilis, a widespread freshwater predator, was used as a model organism. High individual variability was found in the contribution of benthic resources to the isotopic signatures of perch caught in the littoral zone, suggesting substantial within-habitat individual specialization. Small-scale resource origin and 13C enrichment should be accounted for to avoid misleading estimates of both the absolute values and the ontogenetic trajectories of trophic position. A conceptual framework using end-member pathways is proposed to estimate trophic position with the stable isotope technique, particularly when marked ontogenetic niche shifts are expected.