Nowadays the protection of the marine environment raises increasing academic and public attention. The issue of organic micropollutants is of equally high importance for the marine ecosystems. Maritime vessels are considered to significant sources of micropollutants especially if the ship carries many passengers, which is often true for cruise ships which frequent attractive and sensitive sea areas. The emission pathways for micropollutants include wastewater discharges and sewage sludge disposal. The findings of the German research and development project NAUTEK contribute to bridging the knowledge gap about micropollutant emissions from cruise ships. As expected, micropollutants were detected in both the blackwater and greywater on board, emitted from either the passengers or certain ship operations. In total, 16 out of 21 target substances were detected. Peak concentrations of pharmaceuticals could be found mainly in blackwater (peak conc. Carbamazepine 3.9 μg/L, Ibuprofen 29 μg/L, Diclofenac 0.04 μg/L), while greywater is mainly characterized by substances such as ointment residues, UV-filters and flame retardants (peak conc. Diclofenac 0.65 μg/L, Bisphenol A 8 μg/L, Tris(1-chloro-2-propyl)phosphate 136 μg/L). Further analyses suggest a gradual removal of the micropollutants by the onboard MBR plant (MBR effluent peak conc. Carbamazepine 0.47 μg/L, Ibuprofen 6.8 μg/L, Diclofenac 0.3 μg/L). Findings of this research provide a critical stepstone for shaping technical solutions for onboard micropollutants removal and water resource recycling.