Elevated soil salinity and boron levels are critical problems in the San Joaquin Valley of California, affecting crop emergence and yields. With the development of variable rate technology, precision farming offers an alternative for site-specific management of these problems. The objective of this study was to assess soil salinity and boron in cotton fields using the electromagnetic induction (EM) technique and develop management zones for variable seeding application rates. We also compared cotton emergence and yields between variable and uniform seeding rate applications. The variable rate (VR) treatments were applied according to the salinity and boron levels in the fields. The results indicated that the EC levels in the 0-0.3 m soil profile ranged from 0.5 to 14 dS/m. Boron concentrations (1.5 to 8 mg/kg) were typically above the 2 mg/kg threshold for optimum emergence in most areas of the fields. The results also showed that better cotton emergence was observed with the VR treatments. The VR yields were significantly higher from the yields obtained with uniform rate treatments. This study demonstrated that the EM technique provided an accurate estimate of the salinity and the boron levels in soils. The EM results were useful in defining the seeding management zones and subsequently improving the cotton emergence while reducing its variability.