The upper Miocene Chagres Formation, cropping out along the Caribbean coast of Panama, has been previously interpreted as the record of the last deep-water connection between the Caribbean and Pacific oceans based on bodyfossil paleodepth estimates. We test this interpretation by presenting an integrated ichnological and sedimentological analysis on eight coastal localities of the Chagres Formation (Toro Limestone and Chagres Sandstone members). The Toro Limestone Member accumulated under fully marine conditions in a mixed carbonate and siliciclastic marine shelf above storm wave base. Fluctuating high-moderate energy conditions modulated by a combination of tides and high energy currents likely led to the sparse bioturbation of Toro Limestone sediments, corresponding to an archetypal Cruziana ichnofacies assemblage. Bioturbation, dominated by Thalassinoides and Ophiomorpha isp., increases in the overlying Chagres Sandstone Member and corresponds to a proximal expression of the Cruziana ichnofacies. The Chagres Sandstone Member was deposited within the lower shoreface-upper offshore transition zone in a shelf with low sedimentation rates under combined storm, wave, and tidal influence, and includes fossils and sediments of continental origin suggesting proximity to a river mouth. Our results suggest that the Chagres Formation accumulated in shallow waters, contrasting with a previously proposed deep-water accumulation, and are consistent with deposition on a tectonically stable platform of the northern Canal Basin at the apex of the Panama orocline.