The concern about coconut shell disposal and natural fine aggregate depletion has prompted researchers to utilize coconut shell as aggregate in recent years. However, the majority of the present literature has focused on utilizing coconut shell as a coarse aggregate replacement in concrete via the traditional method. In this study, concrete incorporating coconut shell as a fine aggregate replacement (10-100%) was evaluated using permeability and water absorption tests in a systematic way. The response surface methodology (RSM) was first used to design the experimental works. In addition, an artificial neural network (ANN) and genetic expression programming (GEP) were also taken into account to mathematically predict the permeability and water absorption. Based on both experimental and theoretical modeling, three scenarios were observed. In the first scenario, high quality concrete was achieved when the replacement percentage of sand by coconut shell ranged from 0% to 10%. This is because both the permeability and water absorption were less than 1.5 × 10-11 m and 5%, respectively. In the second scenario, an acceptable and reasonable low permeability (less than 2.7 × 10-11 m/s) and water absorption (less than 6.7%) were also obtained when the replacement percentage increased up to 60%. In contrast, the high content coconut shell, such as 90% and 100%, developed concrete with a high permeability and water absorption and was defined in the third scenario. It was also inferred that both the experimental and mathematical models (ANN, GEP, and RSM) have consistent and accurate results. The correlation statistics indicators (R2) were greater than 0.94 and the error was less than 0.3, indicating a strong correlation and minimum error. In conclusion, coconut shell could act as a good alternative material to produce cleaner concrete with an optimum value of 50% as a fine aggregate replacement.