The effects of Canna indica (P1), Pontederia sagittata (P2), and Spathiphyllum wallisii (P3) growing in different filter media materials (12 using porous river rock and 12 using tepezyl) on the seasonal removal of pollutants of wastewater using fill-and-drain constructed wetlands (FD-CWs) were investigated during 12 months. Three units of every media were planted with one plant of P1, P2, and P3, and three were kept unplanted. C. indica was the plant with higher growth than the other species, in both filter media. The species with more flower production were: C. indica > P. sagittate > S. wallisii. Reflecting similarly in the biomass of the plants, C. indica and P. sagittata showed more quantity of aerial and below ground biomass productivity than S. wallisii. With respect to the removal efficiency, both porous media were efficient in terms of pollutant removal performance (p > 0.05). However, removal efficiency showed a dependence on ornamental plants. The higher removal of chemical oxygen demand (COD), biochemical oxygen demand (BOD5), total kjeldahl nitrogen (TKN), nitrates (NO3−-N), ammonium (NH4+-N), and phosphates (PO4−3-P) oscillated between 81% to 83%, 80% to 84%, 61% to 69%, 61% to 68%, 65% to 71%, 62% to 68%, and 66% to 69%, respectively, in P1 and P2, removals 15% to 30% higher than P3. The removal in planted microcosms was significantly higher than the unplanted control units (p = 0.023). Nitrogen and phosphorous compounds were highly removed (60%–80%) because in typical CWs, such pollutant removals are usually smaller, indicating the importance of FD-CWs on wastewater treatments using porous river rock and tepezyl as porous filter media. (BOD5), chemical oxygen demand (COD), (NO3−-N), (NH4+-N), (TKN), and (PO4−3-P).