Waterlogging and salinity impair crops growth and productivity worldwide, being their combined effects larger than the additive effects of both stresses separately. Recently, a new Lotus corniculatus accession has been collected from a coastal area with a high frequency of waterlogging-saline stress events. This population is diploid and has potential to increase nutritional values of Lotus cultivars used as forages. Due to its environmental niche, we hypothesize that this accession would show a better adaptation to combined waterlogging-saline stress compared to another commonly used tetraploid L. corniculatus (cv. San Gabriel). Shoot and root growth under waterlogging, salinity and combined waterlogging-saline treatments were addressed, together with chlorophyll fluorescence and gas exchange measurements. Results showed that salinity and waterlogging effects were more severe for the tetraploid accession, being the differences larger under the combined stress condition. In addition, Na+, Cl− and K+ concentrations were measured in young and old leaves, and in roots. A larger accumulation of Na+ and Cl− was observed under both saline and combined stress treatments for the tetraploid L. corniculatus, for which ion toxicity effects were evident. The expression of the NHX1 and CLC genes, coding for Na+ and Cl− transporters respectively, was only increased in response to combined stress in the diploid L. corniculatus plants, suggesting that ion compartmentalization mechanisms were induced in this accession. As a conclusion, the recent characterized L. corniculatus might be used for the introduction of new tolerant traits to combined stresses, in other Lotus species used as forage.