The performance of an innovative, decentralized, nature-based wastewater treatment system composed of modular units (vermifilters and zooplankton-based reactors) on a pilot scale level (10 p.e.) is presented here. The efficiency of this system was evaluated over a 10-months period under controlled conditions at different flow-rates (750, 1,500 and 3,000 L·d-1). Vermifiltration alone delivered average removals of 88 ± 7%, 89 ± 8%, 91 ± 8% and 85 ± 19% for COD, TSS, NH4+ and BOD5, respectively. Zooplanktonbased reactor provided an important polishing stage that allowed the achievement of removal efficiencies above 95% for TSS, NH4+ and 91% for COD and BOD5, respectively. As the main function of zooplankton-based reactor is to filter fine particles (<30 μm), removal efficiencies of E.coli and turbidity were improved showing the good performance of this reactor as a nature-based tertiary system. The system showed promising results at flow-rates between 750 and 1,500 L·d-1 and only for short periods of time (less than fifteen days) at 3,000 L·d-1. The effluent water obtained was suitable for reuse for different purposes such as agricultural irrigation and process water in conformity with Spanish legislation. These results demonstrate that the integrated system presented here can be used as an eco-sustainable wastewater treatment and also to provide an effluent suitable for reuse.