Periodic flooding of perennial crops such as lucerne (Medicago sativa, L) is a major cause of lowered productivity and leads in extreme cases to plant death. In this study, effects of waterlogging and subsequent recovery on plant nutrient composition and PSII photochemistry were studied to gain a better understanding of the mechanisms of recovery as they relate to leaf photochemistry (chlorophyll fluorescence) and nutrient dynamics. Three lucerne cultivars and one breeding line were flooded for 20 d, drained and left to recover for another 16 d under glasshouse conditions. Leaf and root nutrient composition (P, K, Ca, Mg, B, Cu and Zn) of waterlogged lucerne was significantly lower than in freely drained controls, leaf N concentrations were also significantly lower in waterlogged lucerne. At the same time, there were significantly (5-fold) higher concentrations of Fe in waterlogged roots and Na in leaves (2-fold) of stressed plants. PS II photochemistry, which was impaired due to waterlogging, recovered almost fully after 16 d of free drainage in all genotypes. Alongside fluorescence recovery, concentrations of several nutrients also increased in recovered plants. Growth parameters, however, remained suppressed after draining. The latter was due to both the smaller capacity of CO 2 assimilation in previously waterlogged plants (caused in part by nutrient deficiency and associated inhibition of PSII) and the plant's need to re-direct available nutrient and assimilate pools to repair the damage to the photosynthetic apparatus and roots. It is concluded, that for any lucerne-breeding program it is important to determine not only the degree of tolerance to waterlogging but also the potential for recovery of different genotypes, as well as look for 'outstanding individuals' within each population.Abbreviations: Ci -substomatal cavity CO 2 concentration; ETR -electron transport rate; Fo -minimal fluorescence; Fm -maximal fluorescence; Fv -variable fluorescence; NPQ -non-photochemical quenching; qP -photochemical quenching; qN -non-photochemical quenching; PAM -pulse amplitude modulation; WLwaterlogging; SDW shoot dry weight; RDW -root dry weight.