Inadequately treated wastewater exiting from on-site water treatment systems (OWTS) contains high levels of ammonium and phosphate, which contribute to environmental nutrient pollution. Nutrient removal in small-scale OWTS can be challenging because the most effective known methods are designed for large-scale systems and rely on biological processes. This work focuses on the implementation of two natural silicate-based minerals, clinoptilolite and Polonite, as non-biological sorptive media for nutrient removal in an OWTS. Lab-scale batch sorption experiments showed that Polonite performance is maximized after suspended solids have been removed from blackwater via ultrafiltration. In contrast, clinoptilolite shows robust performance even with untreated blackwater. With both minerals installed in our full-scale OWTS prototype, nutrient removal performance increased from 47.5 ± 15.0% to 84.1 ± 6.3% removal for total N and from 32.3 ± 2.3% to 78.9 ± 5.9% removal for total P. Nevertheless, the target removal performance (>80%) for total P was only achieved with high Polonite loading, which increased effluent pH outside the target range of 6 < pH < 9. Additionally, no loss in nutrient removal performance was observed when the OWTS was restarted after a 150-day idle period. To investigate the potential for media reuse and nutrient recovery, various media regeneration solutions were evaluated. For clinoptilolite, 1 M HCl, NaCl, and KCl all showed good regeneration ability at 2 h contact time, with KCl showing the highest (>86%) ammonium recovery. For the first time, we demonstrated that a minor fraction (30–40%) of binding sites in Polonite can be regenerated using 1 M NaOH or KOH. We also found that the same 1 M HCl regeneration solution could be reused for four clinoptilolite regeneration cycles with no loss in performance. From these results, we discuss opportunities and limitations for implementing these materials in small-scale OWTS.