Management of plant nutrition using fertilizers is an approach to deal with drought and to increase water productivity in paddies. The aim of this study, therefore, was to investigate the effects of nitrogen and potassium fertilizers and drought stress on water use efficiency (WUE) and physiological traits of Gilaneh rice in split-plot experiments based on a randomized complete block design with three replications. Experimental treatments were irrigation intervals (flood irrigation and irrigation at 10 days) as the main factor and different levels of nitrogen (0, 60, and 120 kg ha−1) and potassium (0, 80 and 160 kg ha−1) fertilizers as a subfactor. Results showed that WUE and proline content increased by changing the moisture regime from flood irrigation to 10 days in all levels of fertilizers. The highest WUE (0.764 kg m−3) was observed in the treatment of N fertilizer of 60 kg ha−1 with 160 kg ha−1 of K fertilizer in the 10-day irrigation. The highest plant proline content (16.3 mg g−1 FW) was observed in 160 kg ha−1 of K fertilizer during 10-day irrigation. On the other hand, relative water content, chlorophyll a and b contents, carotenoids, maximum leaf area, and leaf area duration decreased with drought stress at all fertilizer levels. At the stress level, however, the application of fertilizers, in particular N fertilizer treatment, led to improvements in these traits. Given the scarcity of water resources in the country, therefore, WUE and other inputs can be improved in such strategic crops as rice with proper management of plant nutrition.