Aims: Tolerance to waterlogging and recovery ability was compared among the three subspecies of subterranean clover (Trifolium subterraneum L.) to identify tolerance mechanisms, in order to guide future subclover breeding activities. Methods: Three cultivars each of ssp. yanninicum, subterraneum and brachycalycinum were grown in a controlled environment glasshouse with T. michelianum as a waterlogging-tolerant control. After 28 days of growth two treatments were imposed for 35 days: free-draining (control) and waterlogged. A 21-day recovery period followed. Results: After 35 days, waterlogging reduced shoot dry weight (DW) to 58–27% and root DW to 35–21% of respective controls in each subspecies. Shoot relative growth rate (RGR) of yanninicum was least affected (78–104% of control), compared to subterraneum (51–100%) and brachycalycinum (45–69%). The subterraneum cv. Denmark had a similar response to subspecies yanninicum. Shoot RGR of T. michelianum was 138% of its control. After recovery, all traits (except tap root length) recovered to control values. Up to 21 days, the main traits associated with waterlogging tolerance (shoot and root growth) were high petiole length, less petiole anthocyanin pigmentation and high leaf chlorophyll content, but by 35 days these were a high proportion of leaf biomass, high stomatal conductance and enhanced root porosity. Average root diameter and nodulation rates were unrelated to waterlogging tolerance. Conclusions: Subspecies yanninicum had superior waterlogging tolerance. Priority traits for easily-assessed indicators of waterlogging tolerance are less reduction of leaf size and high stomatal conductance.