Exceptionally low river flows are predicted to become more frequent and more severe across many global regions as a consequence of climate change. Investigations of trace metal transport dynamics across streamflows reveal stark changes in water chemistry, metal transformation processes, and remediation effectiveness under exceptionally low-flow conditions. High spatial resolution hydrological and water quality datasets indicate that metal-rich groundwater will exert a greater control on stream water chemistry and metal concentrations because of climate change. This is because the proportion of stream water sourced from mined areas and mineralized strata will increase under predicted future low-flow scenarios (from 25% under Q45 flow to 66% under Q99 flow in this study). However, mineral speciation modelling indicates that changes in stream pH and hydraulic conditions at low flow will decrease aqueous metal transport and increase sediment metal concentrations by enhancing metal sorption directly to streambed sediments. Solute transport modelling further demonstrates how increases in the importance of metal-rich diffuse groundwater sources at low flow could minimize the benefits of point source metal contamination treatment. Understanding metal transport dynamics under exceptionally low flows, as well as under high flows, is crucial to evaluate ecosystem service provision and remediation effectiveness in watersheds under future climate change scenarios.