Climate change-induced flooding has a profound impact on plant growth and development, posing a significant abiotic stressor that significantly affects the yield and quality of cabbage and cauliflower. In many regions, cabbage and cauliflower is severely affected by flooding stress during the cultivation period. This study aimed to assess and compare the effects of flooding stress on the morpho-physiological and biochemical properties of cabbage and cauliflower at different harvest times. In this context, cabbage and cauliflower seedlings were exposed to excess water, and essential parameters, such as photosynthesis, antioxidant enzymes, chlorophyll fluorescence, and certain agronomic features. As a result of flooding stress, significant decreases occurred in agronomic features were measured. The results showed significant decreases in agronomic parameters, including aboveground and underground fresh and dry weights, as well as leaf area. It was observed that the damage rate of plants increased as the exposure time to flooding stress increased. In our experiment, proline, an essential amino acid, significantly increased under flooding stress at different harvest times. Furthermore, the activity of catalase and ascorbate peroxidases, which are reactive oxygen species (ROS), also significantly increased in our investigation. In our experiment, we observed significant increases in proline, an essential amino acid, under flooding stress at different harvest times. Additionally, the activity of catalase and ascorbate peroxidases, which are reactive oxygen derivatives (ROS), also significantly increased. Furthermore, decreases were noted in stomatal conductivity, photosynthetic efficiency, leaf temperature (°C), and chlorophyll fluorescence levels. The application of flooding stress at various harvest times had a negative impact on the growth and development of cabbage and cauliflower plants, leading to significant alterations in their physiological and biochemical properties.