The Concepcion Metropolitan Area (CMA), located on the central coast of Chile, has experienced noticeable wetland loss in recent decades. Our study focused on the Rocuant-Andalien wetland, which has been particularly affected by urbanization. This wetland strongly contributes to flood control, and has provided effective protection against the CMA's latest tsunamis (1835 and 2010). Based on Strategic Environmental Assessment (SEA), we have quantified urban growth over the wetland, both executed and projected under the Metropolitan Urban Plan of Concepcion (MUPC). Recent loss in wetland area by urban growth has been quantified using land use and cover change (LUCC) maps from 2004 to 2014, obtained from the classification of Landsat images. Prospective changes (considering the complete MUPC deployment) have been inferred by combining the MUPC with the 2014 land cover map. In addition, we quantified the observed effect and planned urban growth on the wetland protected area, geoforms and potential flooding based on the area affected by the last Tsunami. Results show that urban areas have increased by 28% between 2004 and 2014, while future increase is expected to reach 238%. In contrast, wetland area has decreased by 10% from 2004 to 2014 and is expected to decrease by up to 32%. Thus, the MUPC is not contributing to the mitigation of wetland loss nor the preservation of its biodiversity and ecosystem services. Implications for coastal planning are discussed.