This paper presents the results of the evaluation of the possibility of using a selected sorbent of natural origin, mineral (opoka rock), for the removal of biogenic compounds from aqueous solutions. The analyzed opoka rock contains approximately 70% calcium carbonate (CaCO3) and from 26 to 27% silicon dioxide (SiO2) and has been classified as heavy opoka rock. The experiment focused on the sorption of organic components, including phosphorus (P), nitrogen (N) and carbon (C). It was carried out for two treatment systems, column tests and batch tests, for three samples of water—water from a water supply system, water from a fish pond and water from a garden pond—located in the region of Silesia (Poland). The results showed that the P removal efficiency was equal to 96.6% for the fine-grained sorbent (grain size < 2 mm) and 90.8% for the coarse-grained sorbent (2–4 mm) in the batch tests, while lower effectiveness was observed for the column tests, reaching 67.8% and 54%, respectively. The efficiency of N (NH4+) removal was equal to 84% for both types of sorbents in the batch tests, while it was 47.7% for the fine-grained sorbent and 26.3% for the coarse-grained sorbent in the column tests. The efficiency of the removal of nitrate-nitrogen (NO3−) was higher for the fine-grained sorbent in all analyzed water samples. The use of materials of natural origin in industrial applications is a recommended direction, part of the green transition. The analyzed samples of opoka rock come from deposits, and opoka rock has so far not been analyzed in terms of its possible use in water and sewage treatment technology. Therefore, further research is recommended for this low-cost sorbent, which may be a competitive material for commercial products.