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Freshwater turtles are essential components of aquatic ecosystems and face unprecedented pressures from habitat destruction, overexploitation, and hydrological alteration. Here, we combined 800 structured interviews with 163 field survey days across 14 provinces in northern Vietnam and Houa Phan Province, Laos (2019–2025), to assess spatial variation in freshwater turtle diversity and community structure. We also focused on the potential temporal shifts in the distribution of the almost extinct Rafetus swinhoei. The surveyed sites were assigned to three zones with different hydrological and habitat features (1 = Red River, 2 = Đà River, 3 = Chu River). A total of 233 verified records represented 11 species, including two non-native taxa (Chelydra serpentina and Trachemys scripta elegans). The assemblage was dominated by Pelodiscus sp. (60.9% of records) and Mauremys sinensis (28.3%), with an overall low diversity (H′ = 1.06). A Whittaker rank-abundance analysis revealed a steep decline in relative abundance after the species ranked 1 and 2, confirming high community unevenness. Zone 1 exhibited the highest Shannon–Wiener index. A Detrended Correspondence Analysis revealed that the three zones are characterised by ecologically distinct turtle assemblages. Chi-square analysis of R. swinhoei records accounting for effect sizes indicated significant spatial and temporal contraction, with recent sightings almost exclusively confined to the Đà River basin. Generalised linear models indicated that dam presence was the strongest predictor of turtle abundance, with zones containing dams exhibiting an estimated 2.57-fold higher total abundance. However, this apparently counterintuitive pattern was due only to Pelodiscus sp. and M. sinensis, two highly generalist species. All other factors showed no significant effect. Collectively, these findings suggest (i) that turtle assemblages are taxonomically distinct across the three zones and (ii) substantial declines in both diversity and distribution, particularly for large softshell species, throughout the whole region.