Born in Cromarty, Miller was a stone mason turned geologist, writer, journalist and religious reformer. He collected and described fossils from many Scottish localities, many of which are now in the Royal Museum in Edinburgh. His 1841 book "The Old Red Sandstone" remains a classic work. He was also a notable collector of Scottish folklore.
Miller started as stone-mason working for his Uncle and came to Edinburgh in 1824 to help rebuild the city after the Great Fire of that year. The dust from the stone damaged his lungs and he returned to Cromarty. Once recovered, he took a job as a monumental mason in Inverness, but soon gave this up to become a bank-clerk. He worked in Edinburgh and Linlithgow, taking the opportunity to examine the rocks of West Lothian for fossils.
Settling in Edinburgh, Miller lived in the Marchmont district of the city and became friendly with geologist Sir Roderick Murchison (1792 - 1871). He became an established writer, particularly noted for his accessible works on geology. He also developed an interest in church affairs, especially the issue of patronage. He became founding editor of a religious newspaper The Witness between 1840 and his death, which was run from offices at 297 High Street.
Miller became a leader of the 'Disruption' of the Church of Scotland in 1843 and his strong religious principles led to his bitter opposition to the emerging theories of evolution. He moved to Portobello in 1852, remaining there until his death. His inability to reconcile his religious views with his scientific research, together with the strain of his work, led to him taking his own life in a bout of depression. He shot himself in his home on Portobello High Street on Christmas Eve and was buried in Grange Cemetery (Edinburgh), following a funeral attended by thousands.
The Scots-American environmentalist John Muir (1838 - 1914) named a glacier in Alaska in Miller's honour.