1699 (MDCXCIX) was a common year starting on Thursday of the Gregorian calendar and a common year starting on Sunday of the Julian calendar, the 1699th year of the Common Era (CE) and Anno Domini (AD) designations, the 699th year of the 2nd millennium, the 99th year of the 17th century, and the 10th and last year of the 1690s decade. As of the start of 1699, the Gregorian calendar was 10 days ahead of the Julian calendar, which remained in localized use until 1923.
- January 19 – The Parliament of England (under Tory dominance) limits the size of the country's standing army to 7,000 'native born' men; hence, King William III's Dutch Blue Guards cannot serve in the line. By an Act of February 1, it also requires disbandment of foreign troops in Ireland.
- January 26 – The Republic of Venice, Polish–Lithuanian Commonwealth and Holy Roman Empire sign the Treaty of Karlowitz with the Ottoman Empire, marking an end to the major phase of the Ottoman–Habsburg wars. The Ottoman Turks cede to Austria all their former territories in Transylvania, Slavonia, Croatia and the whole of Hungary, except for the Banat of Temeswar. The Peloponnese and Dalmatia are ceded to Venice. Large parts of the Ukraine are ceded to Poland. The treaty marks a major geopolitical shift, as the Ottoman Empire subsequently abandons its expansionism and adopts a defensive posture while the Habsburg Monarchy expands its influence.
- February 4 – 350 rebellious Streltsy are executed in Moscow.
- March 2 – The Edinburgh Gazette is first published in Scotland.
- March 4 – Jews are expelled from Lübeck, Germany.
- April 13 – The 10th Sikh Master, Guru Gobind Singh, creates the Khalsa at Anandpur Sahib.
- May 1 – Pierre Le Moyne d'Iberville founds the first European settlement in the Mississippi River Valley, at Fort Maurepas (Ocean Springs, Mississippi).
- June 11 – England, France and the Dutch Republic agree on the terms of the Treaty of London (1700) (Second Partition Treaty) for Spain.
- June 14 – Thomas Savery demonstrates his first steam pump to the Royal Society of London.
- July 6 – Pirate Captain William Kidd is arrested and imprisoned in Boston, Massachusetts.
- July 26 – William Dampier's expedition to New Holland (Australia), in HMS Roebuck, reaches Dirk Hartog Island, at the mouth of what he calls Shark Bay in Western Australia, and he begins producing the first known detailed record of Australian flora and fauna.
- August 25 – Christian V, King of Denmark–Norway since 1670, dies and is succeeded by his son, Frederick IV (to 1730).
- September 22
- December 3 – Baron Jacob Hop is appointed as the treasurer-general of The Hague.
- December 20 – Peter the Great orders the Russian New Year changed, from 1 September to 1 January.
- Billingsgate Fish Market in London is sanctioned as a permanent institution, by an Act of Parliament.
- March 23 – John Bartram, American botanist (d. 1777)
- March 25 – Johann Adolph Hasse, German composer (d. 1783)
- April 17 – Robert Blair, Scottish poet and cleric (d. 1746)
- May 13 – Marquis of Pombal, Prime Minister of Portugal (d. 1782)
- May 14 – Hans Joachim von Zieten, Prussian field marshal (d. 1786)
- June 26 – Marie Thérèse Rodet Geoffrin, French salon holder (d. 1777)
- October 13 – Jeanne Quinault, French actress and playwright (d. 1783)
- November 2 – Jean-Baptiste-Siméon Chardin, French painter (d. 1779)
- November 25 – Pierre Subleyras, French painter (d. 1749)
- November 30 – King Christian VI of Denmark (d. 1746)
- December 19 – William Bowyer (printer), English printer (d. 1777)
- January 3 – Mattia Preti, Italian painter (b. 1613)
- January 14 – Federico Caccia, Cardinal Archbishop of Milan (b. 1635)
- January 21 – Obadiah Walker, English writer (b. 1616)
- January 23 – Kinoshita Jun'an, Japanese philosopher and Confucian scholar (b. 1621)
- January 27 – Sir William Temple, 1st Baronet, English statesman and essayist (b. 1628)
- February 1
- February 20 – Jean-Baptiste Monnoyer, French painter (b. 1636)
- March 12 – Peder Griffenfeld, Danish statesman (b. 1635)
- April 13 – Hans Rosing, Norwegian bishop (b. 1625)
- March 17 – Serafina of God, founder of seven Carmelite monasteries of nuns in southern Italy (b. 1621)
- March 20 – Erhard Weigel, German mathematician, astronomer and philosopher (b. 1625)
- March 27 – Edward Stillingfleet, British theologian and scholar (b. 1635)
- April 21 – Jean Racine, French classic dramatist (b. 1639)
- April 22 – Hans Erasmus Aßmann, Freiherr von Abschatz, German statesman and poet (b. 1646)
- May 12 – Lucas Achtschellinck, Flemish painter (b. 1626)
- May 15 – Sir Edward Petre, 3rd Baronet, English Jesuit, privy councillor (b. 1631)
- May 16 – Christine Charlotte of Württemberg, Regent of East Frisia (b. 1645)
- May 22 – James Bertie, 1st Earl of Abingdon, English nobleman (b. 1653)
- May 25 – Bussy Mansell, Welsh Member of the English Parliament (b. 1623)
- June 1 – George II, Duke of Württemberg-Montbéliard (1662–1699) (b. 1626)
- June 16 – Constantin Marselis, Danish baron (b. 1647)
- June 22
- July 1
- July 2 – Hortense Mancini, favourite Italian niece of Cardinal Mazarin (b. 1646)
- July 10 – Pier Martire Armani, Italian painter (b. 1613)
- August 6 – Albert V, Duke of Saxe-Coburg (b. 1648)
- August 13 – Marco d'Aviano, Italian Capuchin friar (b. 1631)
- August 19 – José Saenz d'Aguirre, Spanish Catholic cardinal (b. 1630)
- August 24 – Lucrezia Barberini, Duchess of Modena (b. 1628)
- August 25 – Christian V, King of Denmark and Norway (b. 1646)
- September 8 – Gottfried Wilhelm Sacer, German jurist (b. 1635)
- September 17 – Augustus, Duke of Schleswig-Holstein-Sonderburg-Plön-Norburg (b. 1635)
- September 26 – Simon Arnauld de Pomponne, French diplomat and minister (b. 1618)
- October 4 – George Evelyn, English politician (b. 1617)
- October 8 – Mary Beale, British artist (b. 1633)
- November 2 – Anthony Ashley-Cooper, 2nd Earl of Shaftesbury, English politician (b. 1652)
- November 23 – Joseph Beaumont, British academic and poet (b. 1616)
- November 29 – Patrick Gordon, Scottish general (b. 1635)
- December 7 – Sigmund von Erlach, Swiss politician (b. 1614)
- December 17 – John Francis Desideratus, Prince of Nassau-Siegen (1652–1699) (b. 1627)
- date unknown