Nitrogen (N) is taken up by most plant species in the form of nitrate (NO$ _3^- $) or ammonium (NH$ _4^+ $). The plant response to continuous ammonium nutrition is species‐dependent. In this study, the effects of the source of N nutrition (NO$ _3^- $, NH$ _4^+ $, or the mixture of NO$ _3^- $ and NH$ _4^+ $) on the response of clover (Trifolium subterraneum L. cv. 45C) plants to prolonged root hypoxia was studied. Under aerobic conditions, plant growth was strongly depressed by NH$ _4^+ $, compared to NO$ _3^- $ or mixed N nutrition, as indicated by the significant decrease in root and shoot‐dry‐matter production (DW), root and shoot water contents (WC), leaf chlorophyll concentration, and chlorophyll fluorescence parameters (F0, Fv/Fm). However, the N source had no effect on chlorophyll a–to–chlorophyll b ratio. Under hypoxic conditions, the negative effects of root hypoxia on plant‐growth parameters (DW and WC), leaf chlorophyll concentration, and chlorophyll fluorescence parameters were alleviated by NH$ _4^+ $ rather than NO$ _3^- $ supply. Concomitantly, shoot DW–to–root DW ratio, and root and leaf NH$ _4^+ $ concentrations were significantly decreased, whereas root and leaf carbohydrate concentrations, glutamine synthetase activities, and protein concentrations were remarkably increased. The present data reveal that the N source (NO$ _3^- $ or NH$ _4^+ $) is a major factor affecting clover responses to hypoxic stress, with plants being more tolerant when NH$ _4^+ $ is the N form used. The different sensitivity is discussed in terms of a competition for energy between nitrogen assimilation and plant growth.