William Aylward had made his fortune in the Newfoundland trade, as had Mr. Rice and Mr. Meagher and, on his death in 1840, his will revealed considerable property interests in the city. The family’s wealth was augmented to a large degree by  the very substantial property held by the Murphy family and, on the death of Ellen’s two unmarried sisters in 1858 all their valuable family and property interests came to the Aylward family. Being raised in such a family where the men and the women were involved in the day-to-day running of their various business interests, Margaret herself became a exceptionally skilled businesswoman – as adept with complex property negotiations, investments and legal matters as she was with the more traditional female accomplishments.   

Although William Aylward had joined with other Waterford citizens in signing a declaration in favour of the Act of Union with Great Britain he was not long in realising his great error and he became a bitter opponent of the Union in later years and he became the confidant and friend of Daniel O’Connell and Thomas Meagher, father of Thomas Francis Meagher. In Glasnevin Convent of the Holy Faith one of Margaret Aylward's most prized possessions was a portrait of Thomas Francis Meagher, autographed thus: "To my dear friend and respected fellow-citizen - Thomas Francis Meagher, October, 1848." The picture was given to her father.

The family had a strong connection with Br Rice and the Christian Brothers in Mount Sion and we have already noted her uncle’s connection. She retained a very high regard for the work of the Brothers all through her life and she was greatly influenced by their service to the poor and the fact that they stayed outside the state system and developed their own curriculum based on Irish children’s needs.  Margaret also had a family connection with the Presentation sisters. In 1797, a fifty year old Waterford woman, Mary Teresa Mullowney from Ballybrack, near Kilmacthomas, had replaced Sr Magdalen Fanning, one of three Waterford women who had journeyed to Cork to receive training in the Cork novitiate of the Presentation convent in Cork. Sr Fanning's health had failed to stand the demands being made on it and she returned home to Waterford. The three who remained, Teresa Mullowney, Eleanor Power and her sister-in-law, Margaret Power, then returned to Waterford, in 1798, to establish the first school for poor girls in her native city. Teresa Mullowney’s brother, John, had been Ellen Murphy’s first husband.

Margaret received her early education in a small Quaker school in Waterford but following the tradition amongst wealthy Waterford families she removed eventually  to the Ursuline Convent in Thurles (then the only boarding school in Ireland for girls) and her brothers were sent to Clongowes Wood and to Stonyhurst (see Thomas Francis Meagher). When Margaret left Thurles, aged twenty, she gave religious instruction to children in the houses of the local gentry such as the Wyses, the Power, the Sherlocks, and she solicited patronage for convent schools. She volunteered, with another lay-person, to teach in the Waterford Presentation convent. She stayed at home in Waterford for four years, teaching in the convent and working in a charity pawn shop, designed to protect the poor of the city from the exorbitant interest rates being charge by the normal pawn shops.  Margaret's sister, Catherine, had joined the Irish Sisters of Charity in Dublin and Margaret also joined, in 1834, receiving the religious name, Sr. Mary Alphonsus Ligouri but her stay there was brief.  An internal dispute split the community and, when the novice mistress was dismissed, thirteen of the twenty-two novices (including Margaret) also left the Order. After residing in Tramore, spending her leisure in teaching children, Margaret,at the age of thirty-five, tried the religious life once again and she joined the Ursuline Order in Waterford city but left, in January 1846, after only two months, finding the loss of liberty too much to bear. She resided for some time with her family at 39, The Mall, Waterford, spending much of her time visiting Dublin, where she had friends amongst the various communities of nuns.

It was in that city that she would labour for the rest of her life. The Great Famine was raging and the city was full of destitute women and children. Margaret joined the Ladies Association of Charity of St. Vincent de Paul and began her mission as a lady visitor, dispensing charity and reading, instructing and praying with the sick poor. In 1851 Margaret founded her own branch of the Charity, centred in the inner city. She came into contact with the work of the Irish Church Missions, a Protestant proselytizing group and vigorously denounced the group. Indeed, she and her Ladies picketed the Sunday schools and were involved in removing Catholic children from Protestant institutions. In 1857, she founded St. Brigid's Orphanage to care for the many orphaned and abandoned children in Dublin. In November 1860, Margaret was sentenced to six months imprisonment and costs after being accused of the kidnapping of a young baby. She was acquitted of the charge but was found guilty of being in contempt of court. The case was a direct result of the struggle between Margaret and the Irish Church Mission. The press divided on religious lines, the Irish Times viciously attacking her and the Morning News defending her as a martyr. The pope, Pius IX, sent her his blessing and a cameo of the Mother of Sorrows as a token of his support.

  In 1851 Margaret had attempted to bring the Daughters of Charity, a French Order, to Dublin but by 1857 she had to admit defeat as the project had not worked as she had planned. This left her with an option that she approached very cautiously and gradually - the founding of a new religious congregation devoted to the care of children on the lines of St. Brigid's. She had the full support of Cardinal Cullen and with his help the 'St. Brigid's Society' was founded. The community that was first known as the Ladies of Charity eventually became the Sisters Of The Holy Faith, though not without some controversy when its founder chose to be answerable only to the Pope, rather than the local bishop. She was an indomitable woman who followed her beliefs through her life, no matter what opposition she encountered on the way. 

Margaret died on 11 October 1889, aged 79 and hundreds of the poor of Dublin walked to the funeral in Glasnevin. Her youngest sister, Jane Fagan wrote 

  My father looked to his son to perpetuate his name, but now - see - it is not his son, but his daughter who will hand it down in honour to posterity.