Submergence is a major factor affecting seedling recruitment in lowland grassland ecosystems. Our aim was to evaluate the tolerance to increasing flooding intensity of the seedlings of tropical grasses Chloris gayana K. and Panicum coloratum L., whose use as a forage species is increasing in humid grasslands. For this purpose, 2-week-old seedlings of C. gayana and P. coloratum were subjected to control, partial submergence (PS) and complete submergence (CS) in clear water for 14 days and allowed to grow for a subsequent 12-day period to assess their recovery. The following responses were assessed: generation of root aerenchyma, morphological changes and emergence from water, biomass allocation in relation to plant size, and biomass accumulation. Results showed that constitutive root aerenchyma was high in both species. Under PS and CS, root aerenchyma increased by up to 50–55% in C. gayana and up to 40–48% in P. coloratum. Under PS, the increase in seedling height for both species was the same as for controls. Under CS, C. gayana further increased its height and emerged more quickly from water; P. coloratum was not able to increase its height, and therefore the seedlings always remained underwater. The escape-from-water response of C. gayana was associated with preferential biomass allocation towards shoots and with a marked lengthening of leaf blades. By contrast, there was no change in allocation in P. coloratum, and its leaves were shorter under CS. The final biomass of C. gayana under CS was similar to that under PS, and equivalent to 54% of its controls. In P. coloratum, biomass under PS and CS were 64 and 21% of its controls (respectively), which indicates that injury caused by CS persisted during the post-submergence period. In conclusion, both species are tolerant to PS at the seedling stage. However, when flood depth increases by submerging the seedlings, C. gayana is able to escape from water while P. coloratum is not, thus strongly affecting its recovery. Therefore, C. gayana appears to be a more promising species for cultivation in lowland grasslands prone to flooding of unpredictable intensity.