Perched on the bow of his long-tail fishing boat, 75-year-old Sukjai Yana untangled a handful of small fish from his net, disappointed by his catch and fretting over whether he can sell them.

Some days Sukjai earns nothing: demand for fish is falling due to worries over contamination of the Mekong River and its tributaries by toxic run-off from rare earth mines upstream that is threatening millions who rely on those waters for farms and fisheries.

Chiang Saen, a fishing hub in northern Thailand,...