The house that stands there today began as a tower house associated with the O'Flaherty clan, the dominant Gaelic family of west Connacht, before passing through a succession of owners whose ambitions for the site grew considerably with each transfer of title. The Martin family, one of the great landed dynasties of Connaught, eventually made Ballynahinch their principal seat, and it was under their tenure that the estate took on the shape that later centuries would recognise.

The most singular figure connected with the house is Richard Martin, known during his lifetime as Humanity Dick, a sobriquet earned through his vigorous campaigning against cruelty to animals. He was among the founders of what would become the Royal Society for the Prevention of Cruelty to Animals, and pushed through legislation at Westminster in 1822 that made the mistreatment of cattle a criminal offence, one of the earliest such laws in the world. The Martin estate at its height was reputedly among the largest private landholdings in Ireland or Britain, stretching across an enormous tract of Connemara, and Ballynahinch sat near its centre. After the Martins, the property passed to the Berridge family and later, in the early twentieth century, became associated with Maharaja Ranjitsinhji, the celebrated cricketer and Indian prince, who used it as a fishing retreat and made improvements to the grounds.