Cotton yield is adversely affected by various stresses including salinity. Genetic variation in salt tolerance is often evaluated in potting soil media irrigated with saline solutions but not a field soil. This study evaluated the efficacy of screening four introgressed Upland genotypes from a backcross Gossypium hirsutum L. × G. barbadense L. inbred line population grown in two soils, i.e., an organic farm loam soil or a conventional farm clay soil. The genotypes were treated with NaCl for three wk at concentrations of 0 or 200 mM starting at the second true leaf stage. Chlorophyll content and fluorescence, plant height, leaf length, main stem node number and internode length, shoot biomass, and number of fruiting sites at three, six and nine week intervals (WT) were measured. Significant genotypic variation at three and six WT was observed, suggesting that salt tolerance screening in early cotton establishment is optimal. The salt treatment had negative effects on all growth traits except chlorophyll content and fluorescence. The organic farm loam soil amended with dairy manure had higher pre-treatment salinity content than the conventional farm clay, resulting in greater initial growth suppression at zero WT. However, the manure-amended soil showed less reduction in vegetative and reproductive growth after more prolonged salt treatment, suggesting that more scrutiny may be needed in soils treated with carbon-based fertilizers. The lack of genotype by soil or treatment interactions suggests that soil type had little bearing in screening cotton genotypes for salt tolerance and that control (non-saline) treatments may not be needed for cotton salt tolerance screening. Finally, this pot study demonstrates that three to six weeks of salt treatments after the second true leaf stage is an adequate duration of time to screen for cotton salt tolerance.