Marine tubular sponges use horizontal suction to receive the nutrients from the perforated body and pump the undigested materials from the top mouth. The idea of a synthetic sponge was inspired by the tubular one. It was introduced to manage the sediment-flow hydrodynamics for enhancing sediment transport in coral reefs and access channels. In the current study, synthetic sponge effects on the dilute sediment concentration were investigated numerically. The Mixture method based on Three-Fluids Modeling (TFM) was selected. The effects of pore area distributions (0–0.42) and jet flow discharges (0–7500 L/h) on the sediment concentration were evaluated. The surface Line Integral Convolution (surfaceLIC) was used as an image processing technique to assess the fluid hydrodynamics. The results indicate that the effects of perforation area distribution are more significant than suction/pumping discharges on the sediment concentration (94.87% vs. 5.13% contribution). So increasing the distribution of perforation areas can effectively reduce water turbidity (between 20% and 50%). The combination of the wide re-circulation zone, Counter Rotating Vortex Pair (CRVP), spiral flow, and dipole formation are the reasons for this. Therefore, the combination of vortices facilitates sediment transport due to the unique shape and mechanism of synthetic sponge.