This study examined the possibility of direct application of phosphate rock (PR) from Lisina deposit, in a mixture with natural clinoptilolite (Cp) and clinoptilolite partially saturated with ammonium ions (NH4–Cp). Solution P concentrations of the NH4–Cp/PR mixtures were sufficient for plant growth and ranged from 0.36 to 0.82 mg L–1. The median NH4–Cp/PR ratio and the longest proposed mixing time had the most positive impact on the P concentration. Solution Ca concentrations of the NH4–Cp/PR mixtures were between 112.5 and 700.5 mg L–1, indicating that use of the proposed NH4–Cp/PR mixtures solves the potential lack of Ca2+ in the solution, which is typical for substrates of similar composition. Selected artificial neural networks (ANNs) were able to predict experimental variables for a broad range of the process parameters all through assay. Manifold effects of small changes in composition of the mixtures and time on the observed concentrations of nutrients were shown using the sensitivity analysis.