Phosphate mining activities on Christmas Island began in the late 1800's providing a unique, long-term case study in which to assess the impacts of mining on coral reef development. Watershed modelling was used to identify potential "hotspots" of mining runoff on to adjacent reefs. Pollution hotspots were also confirmed by analysis of reef sediment. Phosphate rich mining runoff flowed from local watersheds onto nearshore coral reefs with levels of up to 54,000 mg/kg of total phosphate recorded in reef sediment at the Dryers reef site adjacent to the main phosphate storage facility. Using this combination of watershed modelling and in-situ sediment contamination data we identified six coral reef sites along an environmental impact gradient. In-situ benthic transects were paired with a new rubble-encruster method enabling the analysis to combine large scale transect information alongside fine-scale data on epibenthic and encruster assemblages. Results demonstrate that phosphate rich sediment loading negatively impacted coral reef building communities, in particular, branching corals and calcareous encrusting organisms, critical to the future survival of coral reef ecosystems. These findings highlight the importance of curtailing runoff and pollution from catchment based mining activities and protecting reefs for the future.