During the last 20 years, regulatory enforcements regarding with the protection of marine environment have been significantly increased. Especially, starting from 1 January 2010 a new regulation, consisting of waste water treatment plants in ships and new effluent limits, took effect. The new limits comprise a stricter review of prior limits. The strict reduction in the effluent limits for the treated wastewater discharged from ships intimates International Maritime Organization (IMO)'s intention to provide more severe control on wastewater discharges and to demand on installation wastewater treatment system that meet international requirements. Furthermore, the new limits constitute a further challenge for the manufacturing companies specified in design and manufacturing of waste water treatment systems. To way out from these points, this study focuses on development a knowledge-based expert system for selection of appropriate shipboard wastewater treatment system. Within this scope, the study proposes a hybrid approach combining AHP and TOPSIS under fuzzy environment. The three most commonly preferred shipboard wastewater treatment system types are examined and evaluated in terms of various design, operation and environment criteria.