Iron ore was mined from the banded iron formations of Goa, India, and transported through the Mandovi and Zuari estuaries for six decades until the ban on mining from September 2012. Here we focus on the environmental magnetic properties of sediments from the catchment area, upstream and downstream of these estuaries, and adjacent shelf during peak mining time. Magnetic susceptibility (χ lf) and saturation isothermal remanent magnetization (SIRM) values of sediments were highest in upstream (catchment area and estuaries), decreased gradually towards downstream (catchment area and estuaries), and were lowest on the adjacent shelf. The χ lf values of the Mandovi estuary were two to fourfold higher than those in the Zuari. The sediments of these two estuaries after the mining ban showed enrichment of older magnetite and sharp decrease in the SIRM values. Although the input of ore material has been reduced after mining ban, more flushing of estuarine sediments is required for healthier environment.