This study aimed to evaluate the growth, production, and nutrition of naturally colored cotton (cultivar BRS Verde) irrigated with saline water in different growth stages. The trial was conducted with a randomized block design in which the treatments consisted of three irrigation water salinity levels applied throughout the crop cycle or alternately in three growth stages. The lowest-salinity water was drawn from the Arenito Açu aquifer in the state of Rio Grande do Norte, Brazil; the highest-salinity water was prepared to obtain salinity similar to the water drawn from the Calcário Jandaíra aquifer, and an intermediate salinity was obtained from the mixture of equal volumes of the lowest and highest-salinity waters. The application of the lowest-salinity water is recommended in all growth stages due to the increases of about 19% in cotton growth and 40% in yield compared to the application of intermediate or highest-salinity water. The application of the lowest-salinity water in the vegetative stage and the intermediate-salinity water in the following stages is an alternative to using good quality water throughout the cycle, despite the decreases of about 7% in growth and 16% in yield. The nutrition of cotton plants irrigated with saline water throughout the cycle or in some growth stages was marked by an increase of up to 86% in the cotton leaf sodium content, a decrease in the leaf potassium content of up to 21% and increases between 24% and 188% in leaf micronutrient content when the highest-salinity water replaced that with the lowest salinity.