The present work applies for the first time a foraminiferal morphology-based approach (M) and eDNA-based metabarcoding sequencing (G), along with geochemical data to assess the ecological quality status (EcoQS) in the Sepetiba (SE Brazil)</p><p>Highlights:</p><p>Foraminiferal eDNA and morphology are used to infer EcoQS in coastal SE Brazil</p><p>Biotic and abiotic indices show poor/bad EcoQS in the inner area of the Sepetiba Bay</p><p>High/good EcoQS are found in the outer area of the Sepetiba Bay</p><p>Molecular and morpho-methods provide similar EcoQS