Alfalfa cultivation is an effective way to achieve soil improvement while utilizing saline soils. Irrigation and drainage, as physical measures to leach salts, can effectively reduce the soil salt content, while application of organic fertilizer fermented with an effective microorganism (EM) may further enhance the improvement effect of saline–alkaline soil by improving soil fertility and microbial community structure. However, there is still a lack of systematic assessment on the effects of applying these three measures on the saline soil–plant system. In this study, we used alfalfa as the plant material and set three water depths of 8 mm (IR1), 16 mm (IR2), and 24 mm (IR3) under the condition of irrigating every 10 days with remote-controlled timed and quantitative irrigation, which is the most acceptable to farmers in the era of smart agriculture. EM organic fertilizer dosage was designed as 0 kg/ha (CK), 1500 kg/ha (OF1), 3000 kg/ha (OF2), 4500 kg/ha (OF3), and 6000 kg/ha (OF4). The multiple-crop alfalfa yield, quality (crude protein (CP), neutral detergent fiber (NDF), and acid detergent fiber (ADF)), and soil electrical conductivity (EC) were observed. The results showed that after the application of EM organic fertilizer, the soil’s EC value of fertilized treatments was higher than that of CK, but this difference became smaller with the prolongation of alfalfa’s growing period, implying that EM organic fertilizer could absorb more soil salts by promoting alfalfa’s growth; the water depth was obviously negatively correlated with the soil’s EC value, demonstrating that the increase in the water depth had a stronger ability to reduce the soil salts. By the end of the experiment, the soil’s EC values were reduced by 21.4–43.7% for the treatments. The alfalfa yield was significantly increased by EM organic fertilizer application, and the three alfalfa yields were increased by 63.3–69.1%, 65.4–83.6%, and 52.6–56.2%, respectively, when fertilizer application was elevated from CK to OF4. The highest alfalfa yields were all found at IR2OF4, reaching 1164.7, 2637.3 and 2519.7 t/ha, corresponding to the first, second, and third alfalfa crops, respectively. The analysis of alfalfa quality indexes revealed that higher CP values were found in the IR2 treatments, and increasing fertilizer application from OF1–OF4 resulted in an increase in CP values by 2.4–9.1%, 1.5–7.4%, and 0.8–6.7% for the three alfalfa crops. Relatively low NDF and ADF values were observed for alfalfa under IR2 conditions; however, the application of EM organic fertilizer reduced the NDF and ADF values within a certain range. According to the results of the entropy weight evaluation model, IR3OF4, IR3OF2, and IR3OF3 were the top three treatments with the best overall benefits, respectively, with relative closeness values of 0.71, 0.70, and 0.68, in that order, which suggests that the appropriate water depth is 24 mm, while the appropriate EM organic fertilizer dosage is in the range of 3000–6000 kg/ha. There was a pattern observed in our study, in which the treatments with better overall benefits were better distributed at high water depths, which emphasizes the critical role of the irrigation volume in ameliorating saline soils. The conclusions of the study are intended to provide a practical basis for the comprehensive utilization and sustainable development of saline soils.

Reclaiming coastal saline–alkali land is important for food security, yet little is known about how irrigation and biochar jointly affect the fate of fertilizer nitrogen in these soils. Using ¹⁵N isotope tracing, this field experiment tracked the distribution and recovery of labeled fertilizer in a soil–sunflower system under three irrigation quotas (8, 16, and 24 mm per event, applied every 10 days) and four biochar rates (0, 3, 5, and 7 t·ha⁻¹). After harvest, approximately 73% of residual ¹⁵N remained in the 0–40 cm topsoil, with organic-bound N as the dominant fraction (72–74%). Mineral ¹⁵N increased with soil depth, indicating downward movement with water flow. Within sunflower plants, labeled N accumulation followed the order flower head > stem > leaf > root, with heads containing 11–12 times more ¹⁵N than roots, confirming active transport to reproductive organs. Overall ¹⁵N use efficiency ranged from 18.8% to 24.9% across treatments. Increasing biochar rate enhanced ¹⁵NUE by up to 28.2% under the same irrigation regime, whereas raising irrigation from 16 mm to 24 mm reduced ¹⁵NUE by 3.2–3.8%. Mass balance analysis showed that moderate irrigation (16 mm) combined with high biochar (7 t·ha⁻¹) achieved the highest plant ¹⁵N recovery (24.9%), maintained 70.0% of labeled N in soil, and limited unaccounted ¹⁵N to only 5.1%. These findings demonstrate that integrated water–biochar management can optimize fertilizer N retention and crop uptake in coastal saline–alkali soils, providing a scientific basis for precision fertilization in these degraded lands.