This article describes the laboratory-scale manufacture of hydrophobically modified oyster shell powder (mOSP) via a silane coupling agent and used as cement substitutes at 0% to 2.5%. Hydrophobic chemicals have been used in concrete to minimise capillary action by researchers. Although hydrophobic fillers improve concrete's water repellency, replacing fine particles with them in higher proportions has a negative effect. We can use hydrophobically modified fillers in smaller amounts to replace cement while maintaining its critical properties. When mOSP is added in various quantities to binary and ternary mixes with natural zeolite, concrete hydration, mechanical strength, and durability are examined. At a 1.5% replacement ratio, mOSP improved concrete characteristics and durability. With free water and the hydrophobic modified nOSP, concrete mixes were consistently more workable. A gliding effect on the cementitious matrix caused by the surface roughness and hydrophobicity of the developed silane-coated nOSP increases the slump value. The 28-day compressive strength of concrete containing modified nOSP ranged from 39 to 42 MPa without zeolite and 43 to 46 MPa with it. Compressive strength increased more when 10% natural zeolite (NZ) was added with different amounts of mOSP. The RCPT values of the concrete series without zeolite dropped until 1% mOSP replacement (mOSCII), while the 1.5% mix (mOSZIII) had the lowest value. The angularly modified nOSP aggregates interlocked, improving the migration coefficient of mOSP concrete.