The objective of this study was to trace the transformations of phosphorus in an integrated multitrophic aquaculture (IMTA) system and to determine whether the method of plant breeding influenced the dynamics of these changes. In the experiment, the media filled beds (MFB) method of plant cultivation was applied. Fish tanks were stocked with 200 common carp Cyprinus carpio, and hydroponic terraces were planted with 49 zantedeschia Zantedeschia sp. bulbs. Water samples were taken directly from the fish tanks immediately after each type of filtration (mechanical, biological and hydroponic). The basic forms of orthophosphates in the IMTA system included some H2PO4- ions but mostly HPO42-. The higher supply of reactive phosphorus that occurred over time in the experiment may have contributed to a decrease in calcium ion concentration due to the formation of Ca3(PO4)2 and CaHPO4 salts, thus inactivating some of the phosphorus available to plants. Phosphorus may have also been inactivated in the sediment due to the formation of Mg3(PO4)2 and MgHPO4 salts after decreasing the concentration of calcium ions as a result of their precipitation in sediments. Mineralization of organic matter took place under aerobic conditions. Organic matter was a source of biogenic substances in the IMTA system. Experimental results showed that IMTA systems have significant potential to reduce phosphorus in aquaculture wastewater and thus provide a good environment for fish farming by improving water quality.