Mining poses significant and persistent threats to freshwater ecosystems, with impacts often enduring long after operations cease. Growing concerns suggest that the expansion of mining to meet global mineral demands for decarbonization may amplify these cumulative risks to freshwater biodiversity. However, the location and extent of potential conflict hotspots remain poorly understood, hampering our ability to meet international conservation targets. Here, we map areas of potential conflict between freshwater conservation priority areas and global mining activities. Using a spatial modeling approach, we trace potential downstream contamination and quantify the extent of affected river reaches within conservation priority areas. Our analysis reveals that mining may pollute up to 1.8 million km of downstream rivers (5% of the global total), over 18% of which lies within conservation priority areas. Gold mining is associated with the largest extent of potentially contaminated rivers, and its widespread reliance on unregulated small-scale artisanal practices can lead to disproportionately severe impacts on freshwater biodiversity in affected areas. Furthermore, rivers potentially affected by coal mining far exceed those linked to the share of key energy transition minerals needed for clean energy technologies (cobalt, copper, graphite, lithium, nickel, and rare earth elements). Effectively safeguarding and restoring freshwater ecosystems will require conservation and regulatory frameworks that address downstream mining impacts, especially in the context of future mineral expansion.