Natural swimming pools (NSPs) rely on the interaction of bog vegetation, bacteria, and substrate to maintain water quality. Nitrogen (N) and phosphorus (P) levels in NSPs are critical because of their involvement in eutrophication. We conducted a 15-week greenhouse study to address the significant literature gap regarding nutrient removal capabilities of substrates and vegetation in the low-nutrient environment of NSPs. We used mass balance analyses to compare the performances of four substrates [river gravel (control), recycled glass, expanded clay, expanded shale] and two plant species [blue flag iris (Iris versicolor) and lizard’s tail (Saururus cernuus)] under two flow conditions: free water surface and subsurface flow. At the end of the experiment, except for the recycled glass group, all other substrate groups reduced water nitrate (NO3) levels to less than 30 mg⋅L−1, the standard of the 2011 Forschungsgesellschaft Landschaftsentwicklung Landschaftsbau (FLL) guidelines. However, only the expanded clay group closely approached the P standard (≤0.01 mg⋅L−1). Expanded clay and expanded shale demonstrated potential as substrates for NSP bogs. The final aboveground biomass dry weight was strongly negatively correlated with the final NO3 and P water concentrations. However, direct plant uptake proved insufficient to remove all nutrient inputs, especially for P. Except for the recycled glass group (34%), a significant portion of N (79%–90%) from total N added was removed by aboveground biomass. However, P uptake by biomass was substantially lower (18%–37%). With acceptable vigor and biomass accumulation, blue flag iris may be a suitable species for vegetated NSPs, whereas lizard’s tail is not because of uncertain establishment. Compared with controlling N, managing P for FLL standards in NSPs will be more challenging. Our work begins to fill the essential gap in the NSP literature regarding nutrient removal capabilities of substrates and vegetation. Future work should continue to study alternative substrates and plant species for P removal, particularly in field conditions and over longer periods.