Johnes belonged to an old Welsh Carmarthenshire and Cardiganshire family. He was related to William Wilberforce through his mother's aunt Anne Knight. This side of his family can trace to Marchweithian, Lord of Isaled and Aed Mawr, a prince among the first colony of the Britons.

He was the oldest son of Thomas Johnes of Llanfair Clydogau and his mother was Elizabeth, daughter of Richard Knight of Croft Castle, Herefordshire. Born on 1 September 1748, he was baptised at Saint Laurence's Church in Ludlow. After first being taught to read English at a local preparatory seminary in his native town, Johnes attended, at the age of seven, Shrewsbury Grammar School where he remained for four years. In 1760, he was enrolled in Eton where he remained for seven years; during this time he studied the Latin classics and the Greek language under the direction of William Windham. In 1767, he attended a course of lectures on Logic and Moral Philosophy at the University of Edinburgh. Mr. Johnes left Edinburgh in the latter end of the year 1768, and immediately commenced an extensive tour on the continent accompanied by Robert Listen, Esq. Under his guidance, Mr. Johnes proceeded through France, Spain, and Italy. He next proceeded to Switzerland, and following the course of the Rhine as far as Strasburgh, ventured through Alsace and Loraine to Paris, where they took residence for several months.

Returning from the trip in the year 1771, Johnes remained nearly three years in Herefordshire society, and in the rural pursuits suited to his age. In the year 1774, however, tired of a life of pleasure, he was determined to devote himself to more worthy and more important cause; he ran as candidate for the borough of Cardigan and was opposed by Sir Robert Smith. Johnes eventually won by petition.

After completing studies at the University of Edinburgh, Mr. Johnes matriculated at Jesus College, Oxford, where he obtained the degree of M.A. on July 8, 1783. His first acquaintance with Lord Thurlow first occurred while he was at Oxford.

In August 1778 at Saint Mary's Church, Monmouth, Johnes married Maria Burgh, of Monmouthshire, (d. 1782), the only surviving child and heiress of the Rev. Henry Burgh of Parc Llettis. In the same year he was appointed Colonel of the Carmarthenshire militia. Within a year of marriage, Maria fell ill and died at Bath leaving no children.Before the end of that year Mr. Johnes became united in marriage to Miss Jane Johnes, his first cousin who was the daughter of John Johnes of Dolaucothi. This caused a tremendous rift within his family that lead to a total breakdown in their relationship that lasted through the remainder of Johnes's life. It is not clear if he ever spoke with his mother again after his second marriage took place.

His marriage to his wife Jane, a beautiful and highly intelligent woman, brought great happiness to Thomas. They enjoyed a close relationship, sharing an interest in improving Ceredigion and a love of Hafod.

Their first child Mariamné was born 30 June 1784. Johnes was completely besotted with her and was closely involved with her upbringing. No expense was spared in her education; tutors from all over the world were hired. He shared an especially close emotional bond with Mariamné. He was heartbroken when she preceded him in death on 4 July 1811.

His son Evan was born in 1786, during the time his wife Jane had laid the cornerstone of their home. The boy died in infancy.

In the winter of 1814, still grieving the loss of his daughter, and now bankrupt, he became ill and moved to coastal Devon to a house he had recently acquired. He died at Langstone Cliff cottage, near Dawlish on 23 April 1816 aged 68 years. He was buried at Saint Michael's Hafod Church, Eglwys Newydd Parish.

After returning from a tour of Europe in 1774 he was elected MP for the borough of Cardigan in the following year. He went on to be elected MP for Radnorshire in 1780, 1784, 1790, 1795 and for Cardiganshire in 1796, 1802, 1806, 1807, and 1812. He served as Lord Lieutenant of Cardiganshire from 1800 until his death in 1816, was Colonel of the Cardigan Militia, and was elected a Fellow of the Royal Society in 1800.

In 1780, the year he lost his father, in respect for him, he vacated his seat for the borough of Cardigan, and offered himself a candidate for the county of Radnor. This step involved him in a second electioneering contest. He was opposed by Walter Williams, Esq. of Maesclough, but after an heated battle was returned as Knight of the Shire.

The parliamentary politics of Mr. Johnes were at this time decidedly ministerial. To Prime Minister North, who was then prime minister, he was attached by the ties of personal friendship, as well as by their agreement in political views. Like the celebrated Gibbon, he a gave many a silent, but sincere vote in favour of the American war. His devotion was his reward. In the year 1781, he was appointed His Majesty's Auditor for the Principality of Wales. This office, which was in fact a well paid sinecure[sic], was a few years afterwards proscribed by a bill- of reform: but by a kind consideration, usual in such cases, and in this instance enforced by the powerful interference of Mr. Johnes's intimate friend Lord Chancellor Thurlow, its abolition was deferred till the demise of the existing incumbent. While Chancellor, secured for his friend Mr. Johnes, a life interest in the office of Auditor of the Landed Revenues of South Wales, in direct opposition to the report of a Committee of the Commons; the other, as a member of that House, is said, in return, to have contributed by his vote and influence to the reversionary Tellership granted by act of parliament to his noble friend, in express opposition to the wishes of Mr. Fox, with whom he had lately become connected in politics.

In 1780 he inherited the Hafod Estate in Ceredigion from his father as was the case within a landed family. During his first visit to the estate and to Wales he became overwhelmed by the rugged beauty of the area. Upon moving to the estate in 1783, he found it in poor condition, half-ruined, encircled by of Welsh upland. It was populated by a hungry, ill-housed, despairing tenancy. He moved them from huts to cottages and employed many of them planting trees on the property. He had both vision and a pragmatic approach to estate management.

Hafod Uchtryd (meaning the summer place of Uchtryd, a name borrowed from the English word Oughtred) was first known in the 16th century as a farm in the Cwmystwyth, a grange of the monastery of Strata Florida in the valley of the Afon Ystwyth, where the pastures are surrounded by high hills in present day Ceredigion near the Cambrian Mountains of Mid Wales. After the Dissolution of the Monasteries, the farm became the centre of an estate owned by a branch of the Herbert family. It passed by the marriage of the heiress to the Johnes family of Llanfair Clydogau and Dolaucothi.

Mansion

A new mansion at Hafod was build in 1785 by Johnes, after the demolition of the Herbert structure, from the designs of Thomas Baldwin of Bath in the Gothic style. The library was a spacious, octagonal building within the mansion. Johnes collected many rare and noble books on natural history and manuscripts in Welsh, French and Latin, which also included many by Edward Lhuyd and many manuscripts and printed editions of the French chronicles of the later Middle Ages. The library collection of the Marquis de Pesaro was purchased and housed at the estate. A sculpture by Thomas Banks, representing Thetis dipping Achilles in the river Styx stood in the library; The sculpture was commissioned by Mrs. Johnes; the head of Achilles is that of their baby daughter, Mariamne. This work is currently on display at the Victoria and Albert Museum.Adjoining the library was the conservatory in length that was filled with a wide variety of rare plants.Near the entrance from this room into the dining-room hung a painting by Peter Paul Rubens of Decius Mus receiving the Benediction of the Pontifex Maximus. Over the mantel-piece hung a painting of the prophet Elijah fed by the ravens, originally housed at the abbey of Talley, in the county of Carmarthen, and was, on the dissolution of that establishment, given by the superior to an ancestor of Mr. Johnes. Among numerous pictures on display within the mansion were, a portrait of Mr. Johnes of Llanvair, by Sir Godfrey Kneller; of Robert Liston, Esq., by Wickstead; of Richard Gorges, Esq., of Eye, in the county of Hereford; and of Viganoni; a copy of Guido's Cupid Sleeping, landscapes by Both and Berghem, a painting of the ruined Alchymist by Salvator Rosa. In the drawing-room are, Hogarth's celebrated picture of Southwark Fair, a Descent from the Cross by Van Dyck, an "Ecce Homo" by Moralez, two landscapes by Claude, a procession of the Doge of Venice by Canaletti; an Assumption by Bernardo Lonino, pupil of Leonardo da Vinci, which was originally an altar-piece at Lugano; a Holy Family by Reubens, a portrait of Lord Chancellor Thurlow by Gardener, and some beautiful miniatures by the late Miss Johnes. The hall was constructed of Mona marble embellished with a Grecian statue of Dionysus; in addition, six paintings of subjects from Froissart, in imitation of basso relievo, by Stothard.

On 13 March 1807, a fire broke out that completely destroyed the mansion including the contents of the library. Johnes was in London attending Parliament when he heard the news and that his wife and daughter had escaped. The family moved to a rented house in Castle Hill near Aberystwyth. Baldwin of Bath was again hired as architect. On 1 September of the same year, on Johnes's birthday, construction to rebuild the mansion began. Contractors had agreed to pay a heavy financial penalty if the mansion house was not roofed-in by Christmas. Expectant upon moving in Johnes set about replacing the contents of the home. Many of the furnishings were purchased from the Palladian mansion known as Fonthill Splendens, owned by William Thomas Beckford. Interior French glass doors and a number of chimney mantle pieces were purchased, one of which had been sculpted by Banks that featured two couples: Pan and Iris, Penelope and Odysseus. These items were stored at Hafod until the mansion was complete. During construction the family left Castle Hill making tours of London and Scotland, each year returning to find the house unfinished. Construction delays continued until Johnes remained in Wales and made weekly visits, personally overseeing the progress. Altogether the project took three years to complete.

Strongly influenced by William Gilpin's "Picturesque" idea of landscape, which was contrary to the format adopted by the famous Capability Brown, Johnes drew in the experience of his in-laws and family who were from Croft Castle, Herefordshire, his father having married the granddaughter of Richard Payne Knight (1659–1745), a very successful ironmaster whose family acquired land in a fertile part of Herefordshire. The idea of the "Picturesque" developed by Uvedale Price at Foxley and his contemporary (and cousin), Richard Payne Knight's work at Downton were seen by Johnes as a model for the design of his plantations and gardens at Hafod.

Johnes undertook an extensive afforestation on the estate. The number of trees planted from 1796 to 1801 numbered 2,065,000 and continued at a rate of 200,000 per year thereafter. Overall, Johnes planted well over 3 million trees (between ) at Hafod between 1782 and 1813. In 1801 alone he planted half a million trees.

Following a visit to Hafod in 1798, by Charles Howard, 11th Duke of Norfolk, the President of the Royal Society of Arts , Johnes was encouraged to offer himself for the awards made by the Society for silviculture.

Between 1790 and 1810 were the golden years at Hafod. Between 1782 and 1813 approximately 405 to 485 hectares (1000-1200 acres) of forest, mainly European Larch and Scots Pine were planted on high ground, with oak and beech on the lower, more fertile land. In spite of two months of little rain, of the 80,000 Larch planted in April 1796, only 200 died. Following a visit to the estate in 1798 by Charles Howard, 11th Duke of Norfolk, the President of the Royal Society of Arts , Johnes was encouraged to offer himself for the awards made by the Society for silviculture. He was awarded five Gold Medals as follows:

• 1800 - The Gold Medal, being the Premium offered for planting Larch — Trees was this Session adjudged to Thomas Johnes MP of Hafod.
• 1801 — The Gold Medal, being the Premium offered for sowing, planting, and inclosing Timber-trees, was this Session adjudged to Thomas Johnes MP of Hafod.
• 1802 - The Gold Medal, being the Premium offered for sowing, planting, and enclosing Timber-trees was this session adjudged to Thomas Johnes MP of Hafod
• 1805 — The Gold Medal of the Society was this Session adjudged to Thomas Johnes MP of Hafod, in Cardiganshire, for his plantations of Oaks.
• 1810 - The Gold Medal of the Society was this Session adjudged to Thomas Johnes, Esq. MP of Hafod in Cardiganshire, for his Plantations of Larch and other trees.

Approximately three million trees were planted on the estate during the tenancy of Colonel Johnes.

Without doubt, Thomas Johnes was the pioneer of upland afforestation in Wales. However, the achievement was not his alone. Throughout his years at Hafod, Thomas Johnes employed some outstanding foresters and gardeners.

Between 1790 and 1810 two Scottish men played key roles: John Greenshields, Estate Bailiff and James Todd, Head Gardener who had previously been a gardener at the Royal Botanic Garden Edinburgh. These two men were in charge of the extensive plantations and forest-nursery activity.

Over the following years, many more Scots foresters were to play key roles in the development of silviculture on estates throughout Wales. Of course it was the men and boys who did the actual planting thereby, playing a key role in making Hafod an outstanding experiment in land management. At Hafod planting rates were in the order of 1000 per team of one man and a boy per day.

In 1803 Johnes hired James Wyatt, architect of Broadway Tower and Fonthill Abbey, to design a church for the estate to replace the existing structure established in 1620 by William Herbert of the Herbert family, which had fallen into disuse and was surrounded by bramble.

The cruciform structure, constructed at the sole expense of Johnes, was designed in Gothic architecture, has a square tower at the west end. In the centre of the cross is a richly ornamented font of artificial stone, supported on an octagonal shaft; one side of the basin bears a shield charged with the arms of the family of Johnes, and the faces of the shaft are embellished with figures representing the cardinal virtues. A painting, by Fuseli, of Christ and the two disciples of Emmaus is installed in the northern transept. The southern window was composed of an ancient stained and painted Renaissance Flemish glass had been installed in Cardigan Priory church. Johnes removed the window from that church for his own project at Hafod. The window shattered by fire in 1932, and the fragments collected together in small groups.

Several of the Herberts of Hafod are buried in the church graveyard, to whom headstones were erected.

In the fire in 1932, a sculpture monument by Francis Legatt Chantrey, erected to the memory of the late Miss Johnes, which depicted herself and her weeping parents was destroyed after well-meaning fire fighters doused it with water causing it to shatter.

Known today as Hafod Church, it lies within the Vicarage of Llanafan, Aberystwyth. Services are still held at the church every other week in English and Welsh.

New Farm (), an experimental farm including an extensive dairy was established at Hafod. It was thought that the lands of Hafod and surrounding Cardiganshire were of a type of soil that could not support dairy farming, howeber in 1800 approximately four tons of cheese and of butter were produced. Johnes experimented with varieties of cattle to determine which would produce the most milk. In order to accomplish these studies, he imported 40 cows fromHolland which Johnes referred to has his "Dutch ladies." He was subsequently able to produce Parmesan, Stilton, Cheshire and Gloucestershire cheese at will from his own dairy.

Johnes helps to established the Society for the Encouragement of Agriculture and Industry in the County of Cardiganshire as a way to encourage growth in the surrounding area and to promote modern farming techniques to his tenants. He became very frustrated by their refusal to use equipment as basic as a horse and plough, instead preferring pick and shovel. Farming families from Scotland were brought down into Wales to demonstrate productive techniques, but still the local tenants refused to take example.

The Hafod Arms Hotel, in Devil's Bridge was constructed by Johnes as a way to encourage tourism in Cardiganshire. At the time the estate encompassed present day Pontarfynach.

In addition to his concern for social welfare of those at Hafod, he was extremely interested in improving parts of Cardiganshire and actively involved himself in the building of roads and bridges. Upon inheriting the estate there was not one passable road within its boundaries. He built Hafod Arch in 1810 to commemorate George III's golden jubilee. He also built a school for the poor of the community to attend at no charge. A fund was established to assist families hit by casualties. A physician was brought on staff and medicine was supplied. Each year he and Mrs. Johnes opened up their home at Christmas hosting a large event for everyone at Hafod including staff and tenants.

At the suggestion of his wife Jane, Johnes translated several books from French to English. He established a private press (Hafod Press) in a cottage in the hills away from the main estate in order to publish his works:

• A Cardiganshire Landlord's Advice to his Tenants (Original work, translated into Welsh; both editions printed at Hafod Press, 1800)
• Translation of De la Curne de Saint Palaye's Life of Froissart 1803, Volumes I to IV.
• The Chronicles of England, France, Spain Translated from the French of Sir John Froissart, 4 volumes, 1806
• Translation of De Joinville's Memoirs of Saint Louis from French, 1807, 2 volumes, (Printed at Hafod Press)
• Travels of Bertrandon de la Brocquiere in Palestine 1807, 8 volumes, (Printed at Hafod Press)
• The Chronicles of Monstrelet, Notes by the Translator 4 volumes, 1809

Today the Hafod Estate continues to reflect the vision of Thomas Johnes. In Welsh, this is captured in the portmanteau word meaning ‘the landscape with everything in it’ - place, people and nature intertwined.

The Hafod Trust and the Forestry Commission, the current owners, endeavour to preserve and enhance the landscape of Thomas Johnes.