Mortimer's interest in archaeology was aroused as the result of visiting the Great Exhibition and the British Museum during a visit to London in 1851. In company with his brother Robert he began collecting stone tools from the fields of the Yorkshire Wolds. He also trained local farm workers and labourers to identify objects of archaeological interest. Mortimer would pay for these artefacts and stone tools soon became known on the Wolds as "Mortimers".
In 1860 Mortimer's curiosity was excited by the discovery of human remains during the quarrying of a barrow on Painsthorpe Wold. He visited the site repeatedly and made written notes as a result found himself wondering what was inside the many barrows that dotted the Wolds. In May 1863 Mortimer conducted his first actual excavation and by 1896 he and Robert had excavated approximately 360 barrows of Neolithic, Bronze Age or Iron Age date. These excavations were finally published in 1905 as Forty Years Researches in British and Saxon Burial Mounds of East Yorkshire.
In 1877 Mortimer purchased land in Driffield and had constructed at his own expense a museum to house the results of his excavations.
Mortimer died in 1911 and in 1913 the 66,000 piece Mortimer collection of artefacts and geological specimens was sold to Hull Corporation, the purchase being funded by a Colonel G.H. Clarke. It was transferred from Driffield to Hull in 1918 and finally went on display in the Victoria Galleries, Hull on the 1st October, 1929.
The survival of the finds from his excavations, together with Mortimer's notes means that his work resulted in an important body of data for understanding the prehistory of eastern Yorkshire.