Sand mining, which has tripled in the last two decades, is an emerging concern for global biodiversity. However, the paucity of sand mining data worldwide prevents understanding the extent of sand mining impacts and how it affects wildlife populations and ecosystems, which is critical for timely mitigation and conservation actions. Integrating remote sensing and field surveys over 14 years, we investigated mining impacts on the critically endangered Yangtze finless porpoise ( Neophocaena asiaeorientalis asiaeorientalis ) in Dongting Lake, China. We found that sand mining presented a consistent, widespread disturbance in Dongting Lake. Porpoises strongly avoided mining sites, especially those of higher mining intensity. The extensive sand mining significantly contracted the porpoise's range and restricted their habitat use in the lake. Water traffic for sand transportation further blocked the species's river–lake movements, affecting the population connectivity. In addition, mining-induced loss of near-shore habitats, a critical foraging and nursery ground for the porpoise, occurred in nearly 70% of the water channels of our study region. Our findings provide the first empirical evidence of the impacts of unregulated sand extractions on species distribution. Our spatio-temporally explicit approach and findings support regulation and conservation, yielding broader implications for sustainable sand mining worldwide.