Polder watercourses within agricultural areas are affected by high chemical oxygen demand (COD) and biological oxygen demand (BOD 5 ) concentrations, due to intensive farming activities and runoff. Practical cases have shown that constructed wetlands (CWs) are eco-friendly and cost-effective treatment systems which can reduce high levels of organic and nutrient pollution from agricultural discharges. However, accumulated recalcitrant organic matter, originated by in-situ sources or elements of CWs (i.e., plants or microbial detritus), limits the fulfilment of current COD discharge threshold. Thus, to evaluate its relevance regarding rivers ecosystem health preservation, we analysed the response of bio-indicators, the Multimetric Macroinvertebrate Index Flanders (MMIF) and the occurrence of organic pollution sensitive taxa towards organic pollutants. For this purpose, statistical models were developed based on collected data in polder watercourses and CWs located in Flanders (Belgium). Results showed that, given the correlation between COD and BOD 5 , both parameters can be used to indicate the ecological and water quality conditions. However, the variability of the MMIF and the occurrence of sensitive species are explained better by BOD 5 , which captures a major part of their common effect. Whereas, recalcitrant COD and the interaction among other physico-chemical variables indicate a minor variability on the bio-indicators. Based on these outcomes we suggest a critical re-evaluation of current COD thresholds and moreover, consider other emerging technologies determining organic pollution levels, since this could support the feasibility of the implementation of CWs to tackle agricultural pollution.