Sustainably increasing the global food supply in the face of climate change is the utmost important issue that faces the worldwide population. With a changing climate, more prevalent episodes of regional damage due to precipitation and temperature extremes will limit agricultural productivity and may affect the nutritional values of crops. Increasing yields and nutritional values will require implementing novel approaches in gene discovery and plant breeding. The increasing occurrences of extreme precipitation events due to climate change, when combined with the increased global demand for nutritionally rich foods, places pressure on producers to meet demands. Despite being nutritionally rich and increasing in popularity among consumers, the physiological reactions of kale (Brassica oleracea L. var. acephala) to waterlogging conditions are unknown. The purpose of this study was to determine the effects of short-term waterlogging on juvenile kale plants and to identify changes in key nutritional metabolites. Plants harvested after six days of waterlogging demonstrated a 13% decrease in plant biomass when compared to non-waterlogged plants. Waterlogged kale plants also exhibited a decrease in carotenoid (CAR) concentrations of beta-carotene, lutein, zeaxanthin, neoxanthin, and chlorophyll A (ChlA) and chlorophyll B (ChlB) concentrations. Elevated levels of total glucosinolates (GSs) existed for waterlogged kale plants compared to non-waterlogged plants. Of the nutritionally important GSs, elevated concentrations of raphanin, sinigrin, nasturtiin existed for waterlogged plants, and these have been linked to carcinogen-blocking enzymes. Similarly, there were also increased levels of progoitrin and epiprogoitrin which have been linked to health problems such as goiterism. Thus, waterlogging has been shown to decrease the overall nutritional value of kale by decreasing CAR and both chlorophylls while marginally increasing nutritionally important GSs.