Ecological conservation and restoration have increasingly captured attention worldwide due to the degradation of ecosystems. As one of the most ecologically fragile areas, the Tarim River Basin, of Xinjiang, China, encountered serious decline of desert riparian forests. The Chinese government has implemented the "Ecological Water Conveyance Project" (EWCP) since 2000, protecting and restoring the dominant natural species of the desert riparian forests, i.e., Populus euphratica Oliv. The regenerative effect after the water conveyance was noteworthy. For the purpose of clarifying the mechanism of P. euphratica forest regeneration to find a better prescription for the ecological restoration works in the Tarim River Basin, we investigated the relationship between the distribution of P. euphratica and soil salinity. Experimentally evaluated the effects of surface soil salinity on P. euphratica seed germination and the influence of river flooding on the salinity of surface soils. The results showed that (1) P. euphratica trees mainly spread along the river channel within 2 km; with increasing vertical distance to the channel, the number of trees declined significantly; (2) where the salinity of the surface soil is high, there are less living P. euphratica trees; (3) the germination of P. euphratica seeds decreases with increased soil conductivity; when the soil conductivity was higher than 7 ms/cm, the germination of P. euphratica seeds was severely curtailed. (4) Flooding regimes were a pre-condition of P. euphratica restoration; they had profound effects on improving the germination of the seeds via ameliorating water conditions and reducing salinity. Our results point out that the most efficient ecological prescription for restoring and protecting desert riparian forests is to induce flooding twice yearly during June to August with 10- to 15-day durations each time. Such a plan (especially in the Tarim River Basin) should prioritize the protection of seedlings.