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Paddy cultivation in the Dry Zone of Sri Lanka, particularly the Kilinochchi district, faces severe limitations in productivity due to frequent flash floods during the Maha season. Flooding is one of the major causes of crop failure, decreasing average yield, as most locally cultivated varieties have a survival period limited to approximately seven days. In the Kilinochchi region, Farmers lack suitable rice varieties that survive under stress conditions, and 36 Ha of paddy was fully damaged, and 220 ha of paddy was partially damaged during the Maha 2024/2025 season. The study addresses this practical issue by screening local and known tolerant varieties to identify superior germplasm suitable for the region. The main objective was to evaluate the submerge tolerance level of selected rice varieties under controlled conditions and recommend promising rice varieties. Fifteen rice varieties, including twelve commonly cultivated local types and three known tolerant checks (Bg 455, Bg 379-2, Bw 14-7-5), were screened as three-week-old seedlings under controlled 7-day (mild) and 14-day (severe) complete submergence at the Rice Research Station, Paranthan. Under 7-day submergence, the overall mean survival was 79.00%. Tolerant varieties (90.10% survival) exhibited a quiescence strategy with moderate elongation (8.99 cm), whereas susceptible varieties (82.98% survival) employed an escape strategy marked by significantly higher elongation (14.33 cm). For many commonly cultivated varieties in Kilinochchi, survival was limited to ∼7 days of submergence. Under 14-day submergence, the overall survival rate dropped drastically to 20.94%. However, the variety Bw14-7-5 demonstrated the highest tolerance across both stress levels, recording a 94.12% survival rate at 7 days and a superior 39.04% survival rate at 14 days. Based on its consistent and superior performance under both mild and severe submergence stress, Bw147-5 is recommended as the most suitable variety for enhancing rice productivity and resilience in the flood-affected areas of the Kilinochchi district.