Seabed gallery intake systems used for seawater reverse osmosis facilities employ the same principle of water treatment as slow sand filtration in freshwater systems. An investigation concerning the effectiveness of the active layer (top layer) in improving raw water quality was conducted by using a long-term bench-scale columns experiment. Two different media types, silica and carbonate sand, were tested in 1 m columns to evaluate the effectiveness of media type in terms of algae, bacteria, Natural Organic Matter (NOM) and Transparent Exopolymer Particles (TEP) removal over a period of 620 days. Nearly all algae in the silica sand column, 87% (σ = 0.04) of the bacteria, 59% (σ = 0.11) of the biopolymer fraction of NOM, 59% (σ = 0.16) of particulate and 32% (σ = 0.25) of colloidal TEP were removed during the last 330 days of the experiment. Total removal was observed in the carbonate sand column for algal concentration, while the bacterial removal was lower at 74% (σ = 0.08). Removal of biopolymers, particulate and colloidal TEP were higher in the carbonate column during the last 330 days with 72% (σ = 0.15), 66% (σ = 0.08) and 36% (σ = 0.12) removed for these organics respectively. Removal of these key organics through the 1 m thick column, representing the active layer, will likely reduce the rate of biofouling, reduce chemical usage and minimize operating cost in SWRO systems. The data show that the media will require several months at the beginning of operation to reach equilibrium so that high organic removal rates can be achieved. No development of a “schmutzdecke” layer occurred. The experimental results suggest that unlike freshwater slow sand filtration wherein most water treatment occurs in the upper 10 cm, in seawater systems treatment occurs throughout the full active layer depth of 1 m. The results of this study will help in designing and operating seabed gallery intake systems in varied geological conditions.