The stable nitrogen isotope ratios of individual amino acids (SIAA) have recently been used to estimate trophic positions (TPs) of animals in a simple food chain system. However, it is unknown whether the SIAA technique is applicable to complex food web analysis. In this study I measured the SIAA of stream macroinvertebrates and fishes, together with their potential food sources (periphyton: aquatic primary producers; C3 plant litter: terrestrial primary producers) collected from upper and lower sites in two streams having contrasting riparian landscapes. The stable nitrogen isotope ratios of glutamic acid and phenylalanine confirmed that for primary producers (periphyton and C3 litter) the TP was 1, and for primary consumers (e.g., mayfly and caddisfly larvae) was 2. I built a two-source mixing model to estimate the relative contributions of aquatic and terrestrial sources to secondary and tertiary consumers (e.g., stonefly larva and fishes) prior to the TP calculation. The estimated TPs (2.3-3.5) roughly corresponded to their omnivorous and carnivorous feeding habits, respectively. The result provides evidence that the SIAA method is applicable to the analysis of complex food webs, where heterogeneous resources are mixed.