To gain a better understanding on the trophic ecology of New Granada sea catfish, Ariopsis canteri, and their linkage to mangroves, nitrogen and stable carbon isotopes (δ¹⁵N and δ¹³C), as well as Bayesian mixing models, were used to explore trophic dynamics and potential ontogenic feeding shifts across different size classes: class I (8–20 cm), class II (21–32 cm) and class III (>32 cm). The study area was the estuary of the Atrato River Delta, where information about fish ecology is scarce. The δ¹³C of size class I was lower (mean ± s.d. = −24.96 ± 0.69‰) than that of size classes II (−22.20 ± 0.90‰) and III (−22.00 ± 1.96‰). The δ¹⁵N of size class I was lower (mean ± s.d. = 8.50 ± 0.67‰) than that of size classes II (9.77 ± 0.60‰) and III (10.00 ± 0.66‰). Body size was positively and significantly correlated to δ¹⁵N and δ¹³C. Individuals with L_T > 32 cm presented the highest estimated trophic position (3.8). Five‐source mixing models indicated that for class I, the mean estimated contribution of macroalgae was the highest (6%–57% c.i.), and for classes II and III, the mean estimated contribution of macrophytes was the highest (3%–53% c.i. and 4%–53% c.i., respectively). Ontogenetic feeding shifts of A. canteri were confirmed evidencing decreasing intraspecific competition between small and large individuals. Results suggest that mangroves are a nursery and feeding ground habitat for this species and that mangroves support A. canteri mainly due to the substrate/habitat that supports sources in the food webs. These results can be used in ecosystem‐based fishery management focused on the protection of extensive mangrove areas in the southern Caribbean Sea.