We evaluated the water quality of the wetland ecosystem Pateira de Fermentelos (Portugal) within the Water Framework Directive 2000/60/EC and provide ideas for the wetland enhancement. For that purpose, surface water samples were collected in May 2011, at 5 selected sampling sites, and were analysed for physicochemical, chemical and biological parameters, namely temperature, conductivity, pH, nutrients, organochlorine pesticides, heavy metals and macroinvertebrates. An unacceptable water quality situation was observed for the index of macroinvertebrates in points 1 and 2 (Certima river and Ribeira do Pano), where pollution-tolerant Chironomidae and Oligochaeta were dominant taxa, indicating poor water quality. Total phosphors concentration measured in point 1 (Certima) exceeded the limit value three times. Sediments from the study area indicate contamination by zinc and lead and based on toxicity evaluation these metals could cause adverse effects especially in sediments from point 4 (east bank of the wetland). Higher concetrations of organochlorine pesticides (DDE and α-HCH) were detected in sediments from points 3 and 4 (Agueda and on east bank of the wetland), predicting sediment toxicity. The results of this study revealed the urgency of implementing restoration measures needed to restore water quality in the wetland Pateira de Fermentelos not only to meet WFD objectives, but also to guaranty sustainability and increase the resilience of the wetland ecosystem.