Clonal plants are common in frequently flooded habitats because of their resilience to disturbance. We investigated if submergence prior to fragmentation of clones of two clover species reduced survival and regrowth of clonal fragments, and if these fitness parameters were different between genotypes from highly disturbed river forelands and less disturbed coastal dune slacks. We found that soil flooding severely decreased survival and regrowth, and that plants from the more disturbance-prone habitat were less negatively affected by fragmentation. However, internode size was, surprisingly, often negatively correlated with survival after fragmentation, but positively correlated with regrowth. Apparently, contrasting selection pressures exist on internode size in stoloniferous species growing in disturbed habitats.