Flood irrigation is often applied in the arid regions of Northwest China to facilitate the leaching of salts accumulated in the soil during cotton growth in the previous season. This will, in turn, affect the temporal and spatial patterns of soil salinity, and thus cotton germination. To reveal the salinity of the two soil layers (0–20 cm and 20–60 cm), so as to determine the optimal cotton sowing timing, an electronic ground conductivity meter (EM38-MK2) was employed to measure the soil apparent electrical-conductivity (ECa) on different days: 4 days prior to flood irrigation, and, respectively, 6, 10, 15, 20, and 45 days after flood irrigation. Moreover, geostatistical analysis and block kriging interpolation were employed to analyze the spatial-temporal variations of soil salinity introduced by flood irrigation. Our results indicate that: (1) soil salinity in the two layers on different days can be well inverted from binary first-order equations of ECa at two coils (i.e., ECa1.0 and ECa0.5), demonstrating the feasibility of applying EM38-MK2 to estimate soil salinity in the field; and (2) soil salinity in the 0–20 cm layer significantly decreased during the first 15 days after flood irrigation with the greatest leaching rate of 88.37%, but tended to increase afterwards. However, the salinity in the 20–60 cm layer was persistently high before and after flood irrigation, with merely a brief decrease during the first 10 days after flood irrigation at the highest leaching rate of 40.74%. (3) The optimal semi-variance models illustrate that, after flood irrigation, the sill value (C0 + C) in the 0–20 cm layer decreased sharply, but the 20–60 cm Range of the layer significantly increased, suggesting that flood irrigation not only reduces the spatial variability of surface soil salinity, but also enhances spatial dependence in the 20–60 cm layer. (4) The correlation of the soil salinity between the two soil layers was very poor before flood irrigation, but gradually enhanced during the first 15 days after flood irrigation. Overall, for the study year, the first 15 days after flood irrigation was an optimal timing for cotton sowing when the leaching effects during flood irrigation were most efficient, and overrode the effects of evaporation and microtopography. Although not directly applicable to other years or regions, the electromagnetic induction surveys and spatiotemporal analysis of soil salinity can provide a rapid and viable guide to help determine optimal cotton sowing timing.