This study explores a retrospective non-targeted analysis (NTA), based on Ultra High-Performance Liquid Chromatography coupled to High-Resolution Mass Spectrometry (UHPLC-HRMS), to assess hidden chemicals of emerging concern (CECs) in marine model organisms. Conventional ecotoxicological studies do not include evaluating the natural habitats of the collected organisms, missing the possibility of highlighting unexpected pollutants, and thus compromising the correctness and reliability of the experimental results. In this paper we reprocessed samples previously collected from the Venice Lagoon for ecotoxicological studies and used for targeted analysis of three bisphenols-related compounds (i.e. BPS, BPF and BPAF) on seawater and specimens of the clam Ruditapes philippinarum. Results from the validation were the following: accuracy, expressed as percentage recoveries (R%), in the range 80%<R%<120% for all the considered compounds and matrices, and precision, expressed as relative standard deviation of the absolute areas of IS, was <20% for clams (N = 24) and <15% for seawater (N = 30). LODs ranged from 5 to 50 ng/L for seawater and 5–12 ng/g for clam tissues.After validation, a retrospective NTA was carried out on control samples, showing the presence of some CECs, i.e. Lopinavir, Ritonavir, DEHS, and DEHA, two antiviral drugs used during the COVID-19 pandemic and two plasticizers, respectively, reported here for the first time in the Mediterranean Sea. CEC identifications were confirmed by matching MS/MS spectra with libraries. The present study emphasizes the importance of retrospective investigations to describe the contamination scenario of environmental matrices and the related effect in biota, to correctly address studies on model animals, also including possible “cocktail effects”.