Zola was born in Paris in 1840. His father, François Zola (originally Francesco Zola), was an Italian Engineer, born in Venice in 1795, who engineered the Zola Dam in Aix-en-Provence, and his mother, Émilie Aubert, was French. The family moved to Aix-en-Provence in the southeast when Émile was three years old. Four years later, in 1847, his father died, leaving his mother on a meager pension. In 1858, the Zolas moved to Paris, where Émile's childhood friend Paul Cézanne soon joined him. Zola started to write in the romantic style. His widowed mother had planned a law career for Émile, but he failed his Baccalauréat examination.

Zola's 20 Rougon-Macquart novels are a panoramic account of the Second French Empire. They are the story of a family principally between the years 1851 and 1871. These 20 novels contain over 300 major characters, who descend from the two family lines of the Rougons and Macquarts and who are related. In Zola's words, which are the subtitle of the Rougon-Macquart series, they are "L'Histoire naturelle et sociale d'une famille sous le Second Empire"("The natural and social history of a family under the Second Empire").

During his early years, Zola wrote numerous short stories and essays, four plays, and three novels. Among his early books was Contes à Ninon, published in 1864. With the publication of his sordid autobiographical novel La Confession de Claude (1865) attracting police attention, Hachette fired Zola. His novel Les Mystères de Marseille appeared as a serial in 1867.

After his first major novel, Thérèse Raquin (1867), Zola started the series called Les Rougon-Macquart, about a family under the Second Empire.

In 1862, Zola was naturalized as a French citizen. In 1865, he met Éléonore-Alexandrine Meley, who called herself Gabrielle, a seamstress, who became his mistress. They married on the 31 May 1870. She stayed with him all his life and was instrumental in promoting his work. The marriage remained childless. Alexandrine Zola had a child before she met Zola that she had given up, because she was unable to take care of it. When she confessed this to Zola after their marriage, they went looking for the girl, but she had died a short time after birth.

From 1877, with the publication of l'Assommoir, Émile Zola became wealthy; he was better paid than Victor Hugo, for Example. He became a figurehead among the literary bourgeoisie and organized cultural dinners with Guy de Maupassant, Joris-Karl Huysmans, and other Writers at his luxurious villa (worth 300,000 francs) in Médan, near Paris, after 1880. Germinal in 1885, then the three "cities"—Lourdes (1894), Rome (1896), and Paris (1897), established Zola as a successful author.

In Le Roman expérimental and Les Romanciers naturalistes, Zola expounded the purposes of the 'naturalist' novel. The experimental novel was to serve as a vehicle for scientific experiment, analogous to the experiments conducted by Claude Bernard and expounded by him in Introduction à la médecine expérimentale. Claude Bernard's experiments were in the field of clinical physiology, those of the Naturalist Writers (Zola being their leader) would be in the realm of psychology influenced by the natural environment. Balzac, Zola claimed, had already investigated the psychology of lechery in an experimental manner, in the figure of Hector Hulot in La Cousine Bette. Essential to Zola's concept of the experimental novel was dispassionate observation of the world, with all that it involved by way of meticulous documentation. To him, each novel should be based upon a dossier.With this aim, he visited the colliery of Anzin in northern France, in February 1884 when a strike was on; he visited La Beauce (for La Terre), Sedan, Ardennes (for La Débâcle) and travelled on the railway line between Paris and Le Havre (when researching La Bête humaine).

Although Zola and Cézanne were friends from childhood, they experienced a falling out later in life over Zola's fictionalized depiction of Cézanne and the Bohemian life of Painters in Zola's novel L'Œuvre (The Masterpiece, 1886).

In 1888, he took up photography and obtained a near professional level of expertise. Also in 1888, Alexandrine hired Jeanne Rozerot, a seamstress who was to live with them in their home in Médan. Zola fell in love with Jeanne and fathered two children with her: Denise in 1889 and Jacques in 1891. After Jeanne left Médan for Paris, Zola continued to support and visit her and their children. In November 1891 Alexandrine discovered the affair, which brought the marriage to the brink of divorce. The discord was partially healed, which allowed Zola to take an increasingly active role in the lives of the children. After Zola's death, the children were given his name as their lawful surname.

The self-proclaimed leader of French naturalism, Zola's works inspired operas such as those of Gustave Charpentier, notably Louise in the 1890s. His works, inspired by the concepts of heredity (Claude Bernard), social Manicheanism, and idealistic socialism, resonate with those of Nadar, Manet, and subsequently Flaubert.

Captain Alfred Dreyfus was a French-Jewish artillery officer in the French army. In September 1894, French intelligence found information about someone giving the German Embassy military secrets. Anti-semitism caused senior officers to suspect Dreyfus, though there was no direct evidence of any wrongdoing. Dreyfus was court-martialed, convicted of treason, and sent to Devil's Island in French Guiana.

Zola's 1898 article is widely marked in France as the most prominent manifestation of the new power of the intellectuals (writers, artists, academicians) in shaping public opinion, the media and the state.

Zola died on 29 September 1902 of carbon monoxide poisoning caused by an improperly ventilated chimney. His funeral on 5 October was attended by thousands. Alfred Dreyfus initially had promised not to attend the funeral but was given permission by Mme Zola and attended.

The government offered Dreyfus a choice between a pardon (rather than exoneration), which would allow him to go free (provided that he admit to being guilty), or facing a re-trial in which he was sure to be convicted again. Although he was clearly not guilty, he chose to accept the pardon. Zola said of the affair, "The truth is on the march, and nothing shall stop it." In 1906, Dreyfus was completely exonerated by the Supreme Court.

Zola was initially buried in the Cimetière de Montmartre in Paris, but on 4 June 1908, just five years and nine months after his death, his remains were relocated to the Panthéon, where he shares a crypt with Victor Hugo and Alex Andre Dumas. The ceremony was disrupted by an assassination attempt by Louis-Anthelme Grégori, a disgruntled Journalist and admirer of Edouard Drumont, on Alfred Dreyfus, who was wounded in the arm by the gunshot. Grégori was acquitted by the Parisian court which accepted his defense that he had not meant to kill Dreyfus, meaning merely to graze him.

In 1953, an investigation ("Zola a-t-il été assassiné?") published by the Journalist Jean Borel in the newspaper Libération raises the idea that Zola's death might have been a murder rather than an accident. It is based on the revelation of the Norman pharmacist Pierre Hacquin, who was told by the chimney sweeper Henri Buronfosse that the latter intentionally blocked the chimney of Zola's apartment in Paris ("Hacquin, je vais vous dire comment Zola est mort. [...] Zola a été asphyxié volontairement. C'est nous qui avons bouché la cheminée de son appartement.").

The poet is the Artist in words whose writing, as in the racecourse scene in Nana or in the descriptions of the laundry in L'Assommoir or in many passages of La Faute de l'Abbé Mouret, Le Ventre de Paris and La Curée, vies with the colourful impressionistic techniques of Claude Monet and Pierre-Auguste Renoir. The scientist is a believer in some measure of scientific determinism – not that this, despite his own words "devoid of free will" ("dépourvus de libre arbitre"), need always amount to a philosophical denial of free will. The creator of "la littérature putride", a term of abuse invented by an early critic of Thérèse Raquin (a novel which predates Les Rougon-Macquart series), emphasizes the squalid aspects of the human environment and upon the seamy side of human nature.

More than half of Zola's novels were part of a set of 20 collectively known as Les Rougon-Macquart. Unlike Balzac, who in the midst of his literary career resynthesized his work into La Comédie Humaine, Zola from the start, at the age of 28, had thought of the complete layout of the series. Set in France's Second Empire, the series traces the "environmental" influences of violence, alcohol, and prostitution which became more prevalent during the second wave of the Industrial Revolution. The series examines two branches of a family—the respectable (that is, legitimate) Rougons and the disreputable (illegitimate) Macquarts—for five generations.