The problem of wastewater discharged from facilities for soilless plant cultivation is a worldwide problem. So, there is a strong need to find a simple, maintenance-free technological solution. Such a solution may be the use of biofilters or constructed wetlands with “active” filling, which will be a source of carbon for denitrifying organisms. The aim of this study was to evaluate four different types of materials—Oxytree wood chips (Paulownia Clon in vitro 112®), biobased polybutylene succinate derivatives (BioPBS FZ91PB and BioPBS FD92PB), and beech wood chips—as biofilter media and as solid exogenous carbon sources. The highest efficiency of denitrification and dephosphatation (43.11% and 42.48%, respectively) was characterized by the biobased polybutylene succinate FD92PB. The lowest removal efficiency of phosphorus compounds was achieved for beech chips—25.23% and BioPBS FZ91PB—26.42%. The lowest denitrification efficiency—8.8%—was achieved by Oxytree wood chips. The extent of organic matter (COD) repollution in the treated wastewater requires further study. Wood chips were found to release less COD than biobased polybutylene succinate. The research results showed that all tested materials can be a source of carbon in soilless tomato cultivation wastewater treatment. This is a good starting point for further research on selecting appropriate process parameters and creating new solutions for reactor construction.