She was born in Aranjuez during the reign of her paternal grandfather, Charles III of Spain, the eldest surviving child born to her parents. Her father was the second son of Charles III and his wife Maria Amalia of Saxony; her mother, Maria Luisa of Parma was a granddaughter of Louis XV of France through her mother Princess Louise Élisabeth of France. Louise Élisabeth's husband Philip, Duke of Parma, was a younger brother of Charles III. Carlota Joaquina's future husband was a grandson of Mariana Victoria of Spain, sister of Charles III and the Duke of Parma.
The subject of Carlota Joaquina's marriage was arranged by Mariana Victoria and Charles III in the late 1770s when Mariana went to Spain to encourage diplomatic relations between the estranged countries. Carlota Joaquina was to marry the future John VI of Portugal (at that time only an Infante of Portugal), and Carlota Joaquina's uncle Infante Gabriel was to marry the Infanta Mariana Vitória of Portugal, another grandchild of Mariana Victoria of Spain.
On 8 May 1785 Carlota Joaquina was officially married to the future John VI, King of Portugal, Brazil and the Algarves, the second son of Queen Maria I of Portugal and the late King Peter III of Portugal. The marriage was not consummated until 9 January 1790.
In 1788, when his eldest brother Joseph, Prince of Brazil, died, John became the first in line to his mother's throne. Soon he received the titles Prince of Brazil and 15th Duke of Braganza. Between 1788 and 1816, Carlota Joaquina was known as Princess of Brazil. John, her husband, was good-natured, indolent, corpulent and almost as ugly as she was. His religious observances bored her, and they were quite incompatible. Nevertheless, she gave birth to nine children and, because they were all handsome, it was rumoured that especially the younger ones had a different father. After the birth of the ninth child they began to live separate lives, he at Mafra Palace and she at Queluz Palace or Ramalhão Palace. Here it was rumoured that she had bought a retreat where she indulged in sexual orgies.
In 1807, the Portuguese royal family left Portugal for Brazil because of the Napoleonic invasion.
While in Brazil, Carlota Joaquina made attempts to obtain the administration of the Spanish dominions in Hispanic America, a project known as Carlotism. Spain itself was controlled by Napoleon and its kings, her father and brother Ferdinand, were held by Napoleon in France. Carlota Joaquina regarded herself as the heiress of her captured family. Allegedly among her plans was to send armies to occupy Buenos Aires and northern Argentina to style herself "Queen of La Plata". The Portuguese-Brazilian forces, however, only managed to annex the eastern banks of the Rio de la Plata as Cisplatina, which were kept in the Empire of Brazil after 1822 and seceded in 1828 as the Republic of Uruguay.
When the Portuguese royal family returned to Portugal in 1821 after an absence of 14 years, Carlota Joaquina met a country that had changed much since their departure. In 1807, Portugal had lived stably under absolutism. Napoleonic troops and political attitudes fostered by the Cádiz Cortes in Spain had brought revolutionary ideas to Portugal. In 1820, a liberal revolution commenced in Oporto. A constitutional Cortes Gerais had been promulgated, and in 1821 it gave Portugal its first constitution. The queen had arch-conservative positions and wanted a reactionary response in Portugal. Her husband, however, did not want to renege on his vows to uphold the constitution. Carlota Joaquina made an alliance with her youngest son Miguel, who shared his mother's conservative views. In 1824, using Miguel's position as army commander, they took power and held the king a virtual prisoner in the palace, where the queen tried to make him abdicate in favor of Miguel. The king received British help against his wife and son and regained power, finally compelling his son to leave the country. The queen had also to go briefly into exile.
King John VI lived in Bemposta Palace and Queen Carlota Joaquina in Queluz. Though she lived there quietly, she became decidedly eccentric in dress and behaviour. However, their eldest son Pedro, left behind as regent in Brazil, was proclaimed and crowned on 1 December 1822 as its independent Emperor. John VI refused to accept this until he was persuaded by the British to do so, signing in August 1825 the Treaty of Rio de Janeiro by which he and Carlota Joaquina were granted the honorific title of Emperors of Brasil. He died in March 1826. Claiming ill-health, Carlota Joaquina refused to visit his deathbed and started the rumour that her husband had been poisoned by the Freemasons.
Pedro, Emperor of Brazil, now became King of Portugal as well, but knowing that carrying out the duties of both positions would be impossible, Pedro abdicated in Portugal and made his eldest daughter Maria the Queen of Portugal as well as betrothing her to Miguel, his younger brother. In the meantime, Carlota Joaquina's daughter, the Infanta Isabel Maria was to be Regent in Portugal instead of Carlota Joaquina, who ordinarily would have held such a post as Queen Dowager. About two years later the little queen set out for Portugal, only to find upon arrival at Gibraltar that her uncle and fiancé had not only removed the regent, but declared himself King of Portugal.
Queen Carlota Joaquina died at the Queluz Royal Palace, outside of Sintra. It is speculated whether she died because of natural causes or whether she, in fact, killed herself.
Carlota Joaquina married King João VI of Portugal in 1785 and had several children25 April 1775 - 8 May 1785: Her Highness Infanta Carlota Joaquina of Spain
8 May 1785 - 11 September 1788: Her Highness Infanta Carlota Joaquina of Portugal
11 September 1788 - 20 March 1816: Her Royal Highness The Princess of Brazil, Duchess of Braganza
20 March 1816 - 15 November 1825: Her Most Faithful Majesty The Queen of the United Kingdom of Portugal, Brazil and the Algarves
12 October 1822 - 15 November 1825: Titular Queen of Brazil
15 November 1825 - 10 March 1826: Her Imperial and Most Faithful Majesty The Queen of Portugal and the Algarves, Empress of Brazil
10 March - 2 May 1826: Her Imperial and Most Faithful Majesty The Queen Mother of Portugal and the Algarves, Empress of Brazil
2 May 1826 - 7 January 1830: Her Imperial and Most Faithful Majesty The Queen Dowager of Portugal and the Algarves, Empress Dowager of Brazil
29 August 1825 - 7 January 1830: Titular Empress of Brazil
Carlota Joaquina, Princess of Brazil (1994) – Directed by Carla Camurati. Cast: Marco Nanini, Marieta Severo, Vera Holtz, Ney Latorraca and Marcos Palmeira. Tells a summarized tale, mixing history with legend, of the Princess's life, from her childhood until her (mythical) suicide.
O Quinto dos Infernos (2003) – Directed by Wolf Maya. Cast: André Mattos, Betty Lago, Eva Wilma, Marcos Pasquim and Humberto Martins. A television miniseries produced by Rede Globo which tells the tale of the Portuguese Royal Family during their stay in Brazil.