1. Estuaries are critical to the life histories and development of many marine species, and support some of the most productive aquatic ecosystems. But, owing to their geographic accessibility, many estuaries face considerable anthropogenic threats, which can be exacerbated in developing nations. 2. Understanding the ecological implications of anthropogenic activities as a precursor to dedicated conservation activities requires comprehensive assessments of baseline trophic relationships. This study addresses a shortfall in such information for two tropical, coastal ecosystems globally identified as priority areas for biodiversity conservation: the Paranaguá estuarine complex and Cananéia-Iguape estuarine lagoon system in southern Brazil. 3. Ecological relationships were investigated through carbon and nitrogen stable isotope (δ 13 C and δ 15 N) determination in sediments, plant fragments and the muscle tissues of marine species occupying different trophic levels, including benthic invertebrates, This article is protected by copyright. All rights reserved. This is the author manuscript accepted for publication and has undergone full peer review but has not been through the copyediting, typesetting, pagination and proofreading process, which may lead to differences between this version and the Version of Record. Please cite this article as