Variation in response to climatic and edaphic factors has resulted in the geographic differentiation and specific adaptation of lentil germplasm to its environment. The germination of lentil seeds can be affected by waterlogging caused by relay sowing into standing rice crops. Consequently, there is a demand for waterlogging-adapted lentil genotypes, particularly at germination. This experimentation investigated the effects of waterlogging at germination on a germplasm collection. Firstly, two contrasting genotypes, ATC 70876 and Nugget, were waterlogged for six durations (0, 3, 6, 9, 14 and 21 days) in a pot soil system in the glasshouse. Six days of waterlogging was the duration for germination where genotypes showed the largest contrast in germination rate; therefore, this duration was applied to a larger number (127) of genotypes from 11 countries in a screening trial. Finally, all 127 genotypes were grown in pots in the open to phenotype morphological traits (seed size, above-ground biomass, time to flower and maturity). There was significant variation among genotypes, and those originating from Bangladesh had the highest germination at 21.2 %. The heritability of germination on waterlogged soil among genotypes was intermediate at H2 = 44.8 %. Correlations between morphological and physiological traits showed that the capability of seeds to germinate on waterlogged soil was negatively correlated to time to maturity (r = −0.643). It was concluded that genotypes from Bangladesh are adapted to waterlogging at germination. With an intermediate heritability for germination under waterlogging conditions, selection for relay sowing through waterlogging tolerance at germination is practicable.