The goals of this study were to analyze if there is a difference in the stable isotopic ratio (δC and δN) of macrobenthic species sampled at two sandy beaches (one close to a river mouth and the other far from any freshwater input) and to identify differences in the stable isotopic ratio (δC and δN) in different body parts of three representative species of two Brazilian sandy beach macrofaunas: the polychaete Hemipodia californiensis, the mollusk bivalve Donax hanleyanus, and the crustacean decapod Emerita brasiliensis. No significant differences were detected in the δC stable isotopic ratio between the two sites analyzed; however, in the δN stable isotopic ratio, a significant difference was observed. Regarding the intraspecific response of stable isotopic ratio, D. hanleyanus showed a significant difference in carbon among different body part structures, while a trend for significance was observed for nitrogen isotopes. The differences were significant for both isotopes in E. brasiliensis, and no differences were observed among the body part structures in H. californiensis. There were significant differences in E. brasiliensis carapaces with regard to the δN stable isotopic ratio between the muscle and the whole body. Although the δC and δN stable isotopic ratio differs significantly in the digestive tract, muscles, and whole body of D. hanleyanus, such differences were not enough to determine changes in their trophic levels and food sources. Similar stable isotopic ratios were observed in the whole body, proboscis, and teeth of H. californiensis, highlighting this species as the top predator. In conclusion, stable isotopic analysis of benthic trophic structure can be employed as a tool in coastal management plans or environmental impact studies.