Lentils (Lens culinaris) cannot withstand prolonged flooding. This project aimed to study molecular and physiological responses in L. culinaris under flood stress to understand this plant's key mechanisms for flood tolerance. Six- to eight-week-old lentil seedlings were flooded in a growth chamber for four days. On the fourth day, molecular and physiological experiments were conducted on the flooded and control lentil plants. In addition, a morphological study of the stems and leaves using a scanning electron microscope and volatile compound studies (serving as potential biomarkers for flood stress) using GC–MS were conducted. Under flooded conditions in most of the lentil plants, the expressions of the following genes were upregulated: acetyl-CoA carboxylase carboxyltransferase beta subunit (accD), aldolase, and petD-cytochrome b6/f complex subunit IV (PetD). On the other hand, chloroplast copper/zinc superoxide dismutase (SD) and PBA flash photosystem II D1 precursor (psbA) constituted two downregulated genes among most of the plants. Additionally, higher levels of absorbance for soluble sugar, surface roughness, and surface wax deposition were observed in lentils under flooded conditions. Higher wax accumulation leads to higher leaf hydrophobicity, which is a flood-related adaptation. On the contrary, chlorophyll content, catalase activity, and volatile emissions were reduced among flooded lentils, probably due to cell death and reduced photosynthesis. Oxidative damage occurs when cells’ catalase activity is low, meaning cells are unable to detoxify reactive oxygen species. In conclusion, flooding can cause a notable difference in lentils at anatomical, physiological, and molecular levels.