Submerged breakwaters formed by natural rocks dissipate the incident wave energy. Continuous quarrying of rocks has resulted in its depletion, leading researchers to look for alternate materials for the formation of such barriers. Thus, the concept of artificial reef units has evolved which has been gaining importance owing to the flexibility in molding to any desired shapes and sizes, workability and also due to the fact that it creates a habitable environment to marine flora and fauna. From the hydrodynamic performance perspective, artificial reef units are proven to be more efficient in reducing wave transmission on the lee side (e.g., Southern Caribbean shore of Dominican Republic and Vaan Island, Tuticorin, India). A comprehensive experimental investigation to examine the effect of trench width on hydrodynamic characteristics of the submerged reef system was carried out. The trench width was varied by incorporating single, double, and multiple perforated submerged trapezoidal artificial reef units. The focus of the present study is mainly on the influence of the number of reef units, relative crest width, and relative trench width of the submerged reef system on its transmission and reflection characteristics. The relative trench width was found to be an influential factor on wave transmission past the structure, and the least wave transmission was achieved for the reef configuration with eight units. The details of the experimental investigation, results and discussion are reported in this paper.