BACKGROUND: Purple Queen® is an early ripening pomegranate cultivar growing well in soilless cultivation. Substrates have direct effects on plant development and, due to progressive peatland exhaustion, the request for new materials for plant growth is high. OBJECTIVE: The objective of this work was to verify the effects of a new potential substrate obtained from the remediation of marine port sediments on the nutraceutical profile of Purple Queen® fruits, using 50% and 100% of reclaimed sediment. METHODS: The study was carried out determining ellagitannins and polysaccharides obtained from peel after decoction, and anthocyanins in aril juice on fruits from two agronomic seasons. RESULTS: The presence of 100% of the sediment had a partial detrimental effect on fruits size and weight. Compared to a peat-based commercial substrate (control), remediated sediment preserved ellagitannin content and increased the anthocyanin amount (up to 40% higher) and polysaccharide content up to 34% on dry fruit. High molecular weight polysaccharides (>2000 kDa) were identified in all the fruits with glucose and galacturonic acid as the major sugars. CONCLUSIONS: Fruits from plants cultivated only on sediment or in a mixture with 50% of peat showed significant increases of bioactive compounds as stress response in two consecutive seasons.