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The relationship between cities and wetland cover varies across the globe, with some cities converting wetlands to low‐ and high‐density urban cover and others preserving, conserving, or restoring wetlands, or constructing new ones. However, the scientific literature lacks studies relating changes in systemic flood risk in an urban stormwater management systems to changes in wetland cover. Furthermore, whether and how such relationships are affected by changing storm intensity under climate change is unknown. We present a case study on the effects of changes in urban wetland extent and storm intensity on flooding in an urban drainage system in Valdivia, Chile, under several co‐produced future scenarios and historical trends of development. We used data derived from stakeholder workshops and historical landcover to determine four plausible scenarios of urban development, plus one business‐as‐usual scenario, in Valdivia through the year 2080. Additionally, we used historical precipitation data and downscaled climate data to estimate event rainfall from extreme storms in the year 2080. We found that system flood volume and time the system was flooded increased with increasing wetland loss and rainfall volume. Mean rate and hour of peak discharge were unaffected by wetland loss. Infiltration's relative role in reducing flooding diminished as wetland loss increased. Cities may still experience dangerous and/or unacceptable flooding even with extensive wetland coverage and will likely need to pair conservation with additional improvements in their stormwater management systems and contributing watersheds.