Louis was married on 4 January 1802 to Hortense de Beauharnais, the daughter of the deceased general Alex Andre, Vicomte de Beauharnais and his wife Josephine Tascher de la Pagerie. Josephine was the first wife of Louis's brother Napoleon. Thus Hortense was also Louis's step-niece.

Hortense bore Louis's sons Napoleon Charles Bonaparte and Napoleon Louis Bonaparte in Paris, while Louis was in Holland. In 1806, Louis called for his son to be sent to him in Holland, but he was again refused by Hortense, who believed that her son would never be returned to France. When Louis appealed to his brother Napoleon for help, Napoleon sided with Hortense. Napoleon kept the boy in his own court, and he even had him named the heir to the French throne prior to the birth of his own son.

Two major tragedies occurred during the reign of Louis Bonaparte: the explosion of a cargo ship loaded with gunpowder in the heart of the city of Leiden in 1807, and a major flood in Holland in 1809. In both instances, Louis personally and effectively oversaw local relief efforts, which helped earn him the title of Louis the Good.

After his abdication, Louis Bonaparte assumed the title of Count of Saint-Leu (comte de Saint-Leu), which was a reference to his property at Saint-Leu-la-Forêt near Paris. He was appointed as the Constable of France in 1808, a strictly honorary title.

Louis Bonaparte's reign was short-lived, however, which was due to two factors. The first was that Napoleon wanted to reduce the value of French loans from Dutch Investors by two-thirds, meaning a serious economic blow to the Netherlands. The second factor was the one that became the pretext for Napoleon's demand of Louis's abdication. As Napoleon was preparing an army for his invasion of Russia, he wanted troops from the entire region under his control, the allied border countries. This included troops from the Netherlands. Louis, confronted by his brother's demand, refused point-blank. Napoleon then accused Louis of putting Dutch interests above those of France, and removed most of the French forces in Holland for the coming war in the east, leaving only about 9,000 garrison Soldiers in the country. Unfortunately for Louis, the English landed an army of 40,000 in 1809 in an attempt to capture Antwerp and Flushing. With Louis unable to defend his realm, France sent 80,000 militiamen, commanded by Future King of Sweden Jean-Baptiste Bernadotte and successfully repelled the invasion. Napoleon then suggested that Louis should abdicate, citing Louis's inability to protect Holland as a reason. Louis refused and declared the occupation of the Kingdom by a French army as unlawful. On 1 July 1810 Louis abdicated in favor of his second son, Napoleon Louis Bonaparte. He fled from Haarlem on 2/3 July and settled in Austria. Oudinot invaded Holland on 4 July. Napoleon annexed Holland to France by decree (of Rambouillet) on 9 July.

After his Dutch kingdom was taken away from him, the Austrian Emperor Francis I offered him asylum. Between 1811 and 1813, he found refuge in Graz, where he turned to writing and poetry. Louis wrote to Napoleon after the latter's defeat in Russia to request that the Dutch throne be restored to him; however, Napoleon refused. His request to visit the Netherlands was denied several times by King william I of the Netherlands, but King william II allowed him a visit in 1840. Although traveling in the Netherlands under a false name, some people found out that it was their former king, which led to a cheering crowd gathering under the window of his hotel room. It is said that he was quite moved by this demonstration of affection from his former subjects.

After the death of his eldest brother Joseph in 1844, Louis was seen by the Bonapartists as the rightful Emperor of the French, although Louis took little action himself to advance the claim. Louis's son and heir, the Future Emperor Napoleon III, on the other hand, was at that time being imprisoned in France for having tried to Engineer a Bonapartist coup d'état.

Louis Bonaparte died on 25 July 1846 in Livorno, and his remains were buried at Saint-Leu-la-Forêt, Île-de-France.

Louis Bonaparte's early career was spent in the Army, and he served with Napoleon in Egypt. Thanks to his older brother, Napoleon, Louis was given a commission in the French Military, and was promoted to Lieutenant in the 4th Artillery Regiment, and from there he was made Aide de Camp on Napoleon's staff. Napoleon, during his Italian Campaign, recommended Louis to Carnot, and Louis was consequently made a Captain. He later became a General by the age of 25, although he himself felt that he had risen too high in too short a time.