Halophytes are capable of coping with excessive NaCl in their tissues, although some species may differ in their degree of salt tolerance. In addition, it is not clear whether they can tolerate other confounding factors and impurities associated with non-conventional waters. The experiment was performed in a greenhouse with Crithmum maritimum and Atriplex halimus plants, growing on soil and irrigated with two different water types: reclaimed wastewater (RWW) (EC: 0.8–1.2 dS m−1) and reverse osmosis brine (ROB) (EC: 4.7–7.9 dS m−1). Both species showed different physiological and nutritional responses, when they were irrigated with ROB. Atriplex plants reduced leaf water potential and maintained leaf turgor as consequence of an osmotic adjustment process. Atriplex showed higher intrinsic water use efficiency than Crithmum, regardless of the type of water used. In Crithmum, the water status and photosynthetic efficiency were similar in both treatments. Crithmum presented a higher leaf accumulation of B and Ca ions, while Atriplex a higher amount of K, Mg, Na and Zn. Crithmum plants irrigated with ROB presented higher concentrations of 1-aminocyclopropane-1-carboxylic acid and trans-zeatin-glucoside, whereas abscisic acid concentration was lower. Atriplex showed a lower concentration of trans-zeatin-riboside and scopoletin. The characteristics associated to water irrigation did not influence negatively the development of any of these species, which confirms the use of brine as an alternative to irrigate them with conventional waters.