The socio-ecological impacts of large scale resource extraction are frequently underreported in underdeveloped regions. The open-pit Grasberg mine in Papua, Indonesia, is one of the world's largest copper and gold extraction operations. Grasberg mine tailings are discharged into the lowland Ajkwa River deposition area (ADA) leading to forest inundation and degradation of water bodies critical to indigenous peoples. The extent of the changes and temporal linkages with mining activities are difficult to establish given restricted access to the region and persistent cloud cover. Here, we introduce remote sensing methods to "peer through" atmospheric contamination using a dense Landsat time series to simultaneously quantify forest loss and increases in estuarial suspended particulate matter (SPM) concentration. We identified 138 km2 of forest loss between 1987 and 2014, an area >42 times larger than the mine itself. Between 1987 and 1998, the rate of disturbance was highly correlated (Pearson's r = 0.96) with mining activity. Following mine expansion and levee construction along the ADA in the mid-1990s, we recorded significantly (p < 0.05) higher SPM in the Ajkwa Estuary compared to neighboring estuaries. This research provides a means to quantify multiple modes of ecological damage from mine waste disposal or other disturbance events.