Environmental exposure to Burkholderia pseudomallei, the causative agent of melioidosis, remains poorly characterised due to the low sensitivity of conventional detection methods. Here, we develop CRISPR-BEEPs, a sensitive and resource-efficient CRISPR-based assay, and evaluate its performance against conventional culture-based plate inspection using double-qPCR as the reference standard. CRISPR-BEEPs demonstrated higher sensitivity (93.5% vs 19.4%) and high specificity (100% vs 98.0%). We apply the assay to water samples from natural and piped sources across 15,118 km² in northeast Thailand, collected from or near the households of 439 participants with melioidosis. We compared these with households of 190 participants with other bacterial infections and 506 healthy control participants living in the same endemic region who had never developed melioidosis. CRISPR-BEEPs detects B. pseudomallei in 73.3% of groundwater, 32.9% of surface water, and 26.2% of piped water samples, with results comparable to double-qPCR. The improved sensitivity reveals a significant association between environmental detection within 10 km of households and melioidosis risk (OR 2.74; 95% CI:1.38-5.48), an association undetectable using conventional methods. These findings expose critical sanitation gaps and highlight the value of high-resolution environmental surveillance for disease prevention.