Human-induced land subsidence causes many coastal areas to sink centimetres per year, exacerbating relative sea level rise (RSLR). While cities combat this problem through investment in coastal infrastructure, rural areas are highly dependent on the persistence of protective coastal ecosystems, such as mangroves and marshes. To shed light on the future of low-lying rural areas in the face of RSLR, we here studied a 20-km-long rural coastline neighbouring a sinking city in Indonesia, reportedly sinking with 8–20 cm per year. By measuring water levels in mangroves and quantifying floor raisings of village houses, we show that, while villages experienced rapidly rising water levels, their protective mangroves experience less rapid changes in RSLR. Individual trees were able to cope with RSLR rates of 4.3 (95% confidence interval 2.3–6.3) cm per year through various root adaptations when sediment was available locally. However, lateral retreat of the forest proved inevitable, with RSLR rates up to four times higher than foreshore accretion, forcing people from coastal communities to migrate as the shoreline retreated. Whereas local RSLR may be effectively reduced by better management of groundwater resources, the effects of RSLR described here predict a gloomy prospect for rural communities that are facing globally induced sea level rise beyond the control of local or regional government.