In flood plains, cover crops are able to alter soil properties and significantly affect rice nutrition and yield. The aims of this study were to determine soil properties, plant nutrition, and yield of tropical rice cultivated on flood plains after cover crop cultivation with conventional tillage (CT) and no-tillage system (NTS) at low and high nitrogen (N) fertilization levels. The experimental design was a randomized block in a split-split-plot scheme with four replications. In the main plots were cover crops [sunhemp (Crotalaria juncea and C. spectabilis), velvet bean (Mucuna aterrima), jackbean (Canavalia ensiformis), pigeon pea (Cajanus cajan), Japanese radish (Raphanus sativus), cowpea (Vigna unguiculata)] and a fallow field. In the subplots were the tillage systems (CT or NTS). The nitrogen fertilization levels in the sub-subplots were (10 kg/N ha and 45 kg/N ha). All cover crops except Japanese radish significantly increased mineral soil nitrogen and nitrate concentrations. Sunhemp, velvet bean, and cowpea significantly increased soil ammonium content. The NTS provides higher mineral nitrogen and ammonium content than that by CT. Overall, cover crops provided higher levels of nutrients to rice plants in NTS than in CT. Cover crops provide greater yield than fallow treatments. Rice yield was higher in NTS than in CT, and greater at a higher rather than lower nitrogen fertilization level.