Soil salinity is a major problem that reduces the growth and yield of rice, particularly in coastal rice-growing regions such as certain provinces of Cambodia. This study evaluated salinity tolerance in 60 Cambodian rice varieties at germination and seedling stages and combined physiological analyses with genome-wide association study (GWAS) to identify traits and genomic regions associated with salinity tolerance. The screening at the seedling stage showed CAR 11 was a highly salt-tolerant variety in response to salt stress, suggesting this variety could be used in actual salt-affected fields using the transplanting method and may also serve as a valuable genetic resource for salt-tolerance breeding. K ⁺ concentration and Na ⁺ /K ⁺ ratios in roots and shoots were identified as physiological traits determining salt tolerance of Cambodian rice varieties. Several varieties also exhibited high tolerance during germination under salt stress, suggesting their potential value as genetic resources for salt-tolerance breeding. GWAS identified some marker-trait associations and putative candidate genes associated with salinity tolerance-related traits under salt stress. These findings provide fundamental knowledge regarding salt tolerance and putative genes associated with traits in Cambodian rice varieties, and this knowledge is essential for developing salt-tolerant varieties via breeding programs and extending rice production in salt-affected areas.