Application of common leaching and flushing methods is often impractical due to freshwater scarcity, groundwater pollution and a lack of suitable drainage systems. To address these problems, a pot experiment testing the cultivation of Salicornia persica Akhani was conducted in three replicates. Three saline irrigation treatments (EC = 7.2 dS m−1) were used: full irrigation with saline water (SI), deficit irrigation with 75% of SI (DSI75) and deficit irrigation with 55% of SI (DSI55). Two soil conditions also were considered, namely a combination of soil with 10% composted cow manure (CM) and soil without manure (WA). Our results show that the highest values for stem diameter (3.1 mm), height (110.1 mm) and dry weight (0.5 g) were observed in SI–CM. Conversely, the highest values for root length with 16.9 mm and root weight with 0.7 g were obtained for DSI75-CM. The best treatment for water-use efficiency (WUE) was DSI75-CM with 2.6 g l−1, and the lowest WUE of 1.33 g l−1 was observed for DSI55-WA. DSI increased all examined chemical parameters. The use of CM only resulted in increased values of carbohydrate, protein and proline, with no significant effects found for other parameters. Significant reductions in both EC (38.6%) and Na+ (16.8%) occurred in both soil treatments, with reductions under WA higher than reductions under CM. Overall, our results suggest that the proposed methods could be used for decreasing soil salinity levels while simultaneously allowing for the use of saline water for agricultural production.