The aim of this study focused on the evaluation of constructed wetlands (CWs) microcosms, on a laboratory scale, for the removal of metals from a pig industry effluent while maintaining effluent organic matter and nutrients levels for its later used as a fertilizer. CWs with different macrophytes (Phragmites australis and Typha latifolia) and different substrates (light expanded clay aggregate and lava rock) were tested. Results showed high removals of metals during CWs treatment, with removal rates reaching >80% for Cd, Cr, Cu, Fe, Mn, and Zn after 2 days of treatment in CWs planted with T. latifolia and >60% in CWs planted with P. australis. Significant differences were only found between substrates for Fe and Mn in CWs with P. australis. Removal of organic matter (through chemical oxygen demand (COD)) was >77%, with no significant differences between substrates or plants. Removals of ammonium and phosphate ions ranged between 59–84% and 32–92%, respectively, in CWs with P. australis and 62–75% and 7–68% in CWs with T. latifolia, with no significant differences between substrates. Overall, CWs showed potential to be efficient in removing toxic contaminants, as metals, while maintaining moderated levels of nutrients, allowing the use of reclaimed water in agriculture, namely as fertilizer. If one aims for a short CW treatment, CW planted with T. latifolia and expanded clay as substrate could be the more suitable choice.