In 1784 Narváez went to New Spain, his first assignment being at Havana. For three years he served aboard supply ships working the ports of Veracruz, New Orleans, Mantanzas, Campeche, Roatán, and Trujillo. In November, 1787, he was promoted to segundo piloto havilitado (qualified second pilot) and reassigned to San Blas, at the time the main Spanish naval base on the west coast of Mexico. He arrived in early 1788. Within the month he sailed north as a pilot to Gonzalo López de Haro on the San Carlos
On June 30, 1788, Haro sent Narváez in a longboat to investigate a Russian post at Three Saints Bay, Kodiak Island. Narváez found the post, becoming the first Spaniard to make contact with a large contingent of Russians in Alaska. The Russian commander, Evstrat Delarov, accompanied Narváez to the San Carlos, where he was given a barrel of wine and other gifts. Narváez then returned Delarov to his outpost. Delarov gave Narváez a Russian map of the Alaskan coast and indicated the locations of seven Russian posts containing nearly 500 men. Delarov also told Narváez that the Russians intended to occupy the port of Nootka Sound, on the west coast of Vancouver Island. Narváez returned to the San Carlos and Haro returned east, rejoining Martínez at Sitkinak Island.
Using the information acquired by Narváez, the expedition sailed southwest to investigate Unalaska Island, where there was a large Russian post under the command of Potap Kuzmich Zaikov. Martínez arrived on July 29, Haro on August 4. Martínez and others came ashore and stayed at the post. He provided a supply of foodstuffs and wine. Zaikov gave Martínez three maps covering the Aleutian Islands. He also confirmed that the Russians planned to take possession of Nootka Sound the next year.
Martínez, prone to bouts of abusive aggression, had continuing problems with his officers and sailors, including Haro and Narváez. While at Unalaska, Martínez had Haro temporarily arrested, during which time Narváez was in command of the San Carlos. Haro was restored to his command before the expedition left Unalaska on August 18, 1788. Within three days the two ships broke off contact and sailed south separately. Haro's orders were to rejoin Martínez at Monterey, California, but on the way Haro, with support from Narváez and the other pilots, declared his ship no longer under Martínez's command. They sailed back to San Blas on their own, arriving on October 22, 1788. Martínez, who spent a month in Monterey waiting for Haro, did not arrive at San Blas until December, where he found himself faced with charges of irresponsible leadership. Nevertheless Martínez regained favor and was placed in charge of a new expedition to occupy Nootka Sound before the Russians did.
On June 21, Martínez dispatched Narváez in the captured Northwest America, renamed Santa Gertrudis la Magna (and later Santa Saturnina), to explore three inlets south of Nootka Sound — Clayoquot Sound, Barkley Sound, and the Strait of Juan de Fuca. Narváez sailed more than 25 leagues (about ) into the Strait of Juan de Fuca. Only a few non-natives had entered the Strait by this time, and none as far as Narváez. By early July he was back at Nootka Sound. His report to Martínez recommends Port Renfrew as a good anchorage.
While Narváez was away on this mission, Martínez performed an elaborate ceremony of possession at Nootka and soon after fought a brawl with the British Captain James Colnett, had him imprisoned, and seized several English ships and their crews. These events escalated into a major international crisis. Martínez forced a group of captured Chinese workmen to construct Fort San Miguel and other structures. In July, shortly after Narváez had returned, Martínez captured a newly arrived English ship, the Princess Royal, which led to an incident in which the Nuu-chah-nulth ("Nootka") Chief Callicum, the son of Chief Maquinna, was shot and killed.
Martínez believed that the Strait of Juan de Fuca was the entrance of the legendary Northwest Passage and therefore of extreme strategic importance. On July 27, Martínez placed Haro and Narváez in command of the San Carlos and the captured Princess Royal and sent them back to San Blas with the news. They arrived by the end of August, 1789. In October, Martínez completely evacuated Nootka Sound and returned to San Blas himself, with his prisoners and captured ships.
Eliza arrived at Nootka on April 4, 1790, and found no ships present. The Nuu-chah-nulth natives, alienated by the events of the previous summer, had moved to a more secure location. After reoccupying Fort San Miguel and other buildings, Eliza dispatched two exploration expeditions. Fidalgo explored northward to Alaska on the San Carlos, while Quimper, with López de Haro and Juan Carrasco as pilots, explored the Strait of Juan de Fuca with the Princesa Real. Both ships were unable to return to Nootka and instead sailed to San Blas. Eliza would not know about their discoveries until the following year. After these ships had left Caamaño, with Narváez, arrived on the Aranzazu. He would remain under Eliza's command for the next two years, participating in various voyages of exploration.
The expedition first stopped at Clayoquot Sound, staying for about two weeks. Narváez and Carrasco spent a week exploring the inner channels, and another week collaborating on a chart of the sound, which they called Puerto Clayucuat. While Narváez was busy with this work, Eliza made friends with Chief Wickaninnish. Eliza wrote that he was honored with a dance of over 600 young men. Eliza also reported that there were five large settlements in Clayoquot Sound, each with over 1,500 inhabitants. The largest, which Eliza called Guicananich (Wickaninnish), had over 2,500 people.
In late May Eliza, on the San Carlos, sailed into the Strait of Juan de Fuca to Esquimalt. The Santa Saturnina spent several weeks exploring Barkley Sound. The two ships rejoined at Esquimalt on June 14, 1791.
In the Santa Saturnina Narváez and Carrasco explored the inner channels of Barkley Sound, which they called Puerto de Boca Carrasco, and drafted a chart. According to Eliza's summary report of the voyage, Narváez saw five large settlements with "warlike and daring" inhabitants. On two occasions Narváez's ship was attacked by groups of about 200 men, but "he held them in check by means of some cannon shot." The natives "were surprised to see the schooner and, according to their explanations, had never seen a vessel inside."
In mid-June, with the expedition based at Esquimalt ("Cordova" to the Spanish), Eliza instructed Pantoja to explore Haro Strait with the Santa Saturnina and the longboat. He was assisted by Narváez, Carrasco, and Verdía. They entered the strait and rapidly passed between Vancouver Island and San Juan Island and reached Pender Island. They noted several openings leading west and two leading east, and decided to investigate the larger of the two eastern ones, today called Boundary Pass. On June 15, 1791, they weighed anchor and sailed east along the southern shore of Pender Island and Saturna Island before entering "a grand and extended canal" — the open water of the Strait of Georgia, which they named Canal de Nuestra Señora del Rosario. This was the first time Europeans had seen the Strait of Georgia. The Spaniards believed they had found the legendary inland sea and that it probably connected, somehow, to Hudson Bay or the Mississippi River. They spent the night anchored at Patos Island. The next day they sailed east to the vicinity of Lummi Island and the northern end of Rosario Strait. Out of food and exhausted, they returned they way they had come. The longboat, rowing against the wind, arrived at Esquimalt on June 24, Narváez in the Santa Saturnina the next day.
Eliza moved his base of operations to Puerto de Quadra (Port Discovery) on the south side of the Strait of Juan de Fuca. Eliza and the San Carlos remained there while the Santa Saturnina and the longboat, under Narváez with Carrasco as pilot, set out to explore Rosario Strait and the Strait of Georgia more fully.
Narváez set out on July 1, 1791. Passing through Rosario Strait, which he called Canal de Fidalgo, Narváez surveyed Guemes Island (Islas de Guemes), Cypress Island (San Vincente), and Lummi Island (Pacheco), explored Padilla Bay (Seno Padillo) and Bellingham Bay (Seno Gaston), and anchored in Chuckanut Bay (Puerto Socorro), before heading north into the Strait of Georgia. He anchored in Birch Bay (Puerto del Garzon) and Drayton Harbor (Punta de San José), and sailed west across Boundary Bay to round Point Roberts. For some reason Narváez had the impression that Point Roberts was an island (Isla de Zepeda) and the inland sea extended far to the northeast. On the map later made by Carrasco a large inlet is shown, called Boca de Floridablanca (also Canal de Floridablanca), which included Boundary Bay and extended north to about Burrard Inlet. After rounding Point Roberts Narváez sailed several miles from the shore through the discharge of the Fraser River. He noted the water was "more sweet than salt", but mistook the land between the mouths of the river as low-lying islands in the imagined Boca de Floridablanca. He anchored off Point Grey, which he also took to be an island (Isla de Langara).
While at anchor off Point Grey the Santa Saturnina was visited by a number of Musqueam men in canoes who traded food, water, and firewood for pieces of copper and iron. The Spaniards noted that the language of the Musqueam was quite different from that of the Nuu-chah-nulth (Nootka), which they were familiar with. The Musqueam were able to indicate that the Strait of Georgia continued north for a great distance. One of Narváez's crew bought a young native boy, from whom the Spaniards learned that many Indians regularly came to the Musqueam on horseback, from a "flat country" in the northeast, to trade iron, copper, and blue beads for fish. The Spaniards did not visit the Musqueam village, but did go ashore near Point Grey, where they collected water from a large river (probably the north arm of the Fraser River). Narváez sailed some distance into Burrard Inlet, today the harbor of Vancouver. Carrasco's map shows not only the Musqueam village at Point Grey but another settlement at Point Atkinson (Punta de la Bodega), and another on the entrance to Howe Sound (Bocas del Carmelo), near present-day Horseshoe Bay.
Narváez continued north to Texada Island, Hornby Island, and Denman Island. Nanaimo Harbour was found and named Bocas de Winthuysen. Sailing along Galiano Island and Valdes Island Narváez noted Porlier Pass and gave it its present (Anglicized) name. Narváez's returned to Port Discovery on July 22, 1791.
At the start of his voyage, Narváez had passed by Admiralty Inlet (Ensenada de Caamaño), the entrance to Puget Sound. He planned to explore it upon his return, but was running out of food by then and so returned directly Eliza's San Carlos in Port Discovery. Once resupplied with food from the San Carlos an exploration of Puget Sound was certainly possible, but Eliza was eager to return to Nootka. Thus the Spanish missed the opportunity to preempt the British exploration of Puget Sound, which was done the following year under George Vancouver.
Eliza was impressed by Narváez's report on the size and nature of the Strait of Georgia. A great number of whales had been seen in the Strait of Georgia, but few in the Strait of Juan de Fuca, which led Eliza to later speculate, correctly, a second connection to the ocean. Further, Eliza came to suspect, again correctly, that Nootka Sound was not on the mainland, but rather on an island. Narváez had been unable to explore all of the Strait of Georgia, and Eliza was aware of the importance of further exploration, but by the time Narváez returned to Port Discovery many of Eliza's sailors were sick, as was Eliza himself. Further exploration was abandoned and the ships soon sailed for Nootka. Eliza transferred Narváez to the San Carlos and gave Juan Carrasco command of the Santa Saturnina for the return voyage.
Sailing west, the ships found Port Angeles on August 2, 1791. They reached Neah Bay on August 7. From there the San Carlos, with Narváez on board, returned to Nootka Sound, arriving on November 9. Carrasco, however, was unable or unwilling to beat upwind to Nootka and instead sailed the Santa Saturnina south to Monterey, California, arriving there on September 16, 1791. Alessandro Malaspina was in Monterey at the time, having arrived five days earlier. Thus Malaspina, a powerful figure of the Spanish navy at the time, became the first to know about the discovery of the Strait of Georgia, outside of Eliza's sailors at Nootka Sound. Malaspina immediately recognized the strategic importance of further exploration. Shortly after his encounter with Carrasco, Malaspina sailed to San Blas and Acapulco, where he arranged to have two of his own officers, Dionisio Alcalá Galiano and Cayetano Valdés, take command of two ships for the purpose of fully exploring the Strait of Georgia.
Eliza eventually received credit for most of the discoveries made during the 1791 expedition under his command, even though he actually did no exploring himself and Narváez commanded the ship that made most of the discoveries.
Narváez arrived at San Blas on November 1, 1810, in command of the frigate Activo. Within days he was ordered by Commander Lavayen to arm the ship for war and load it with supplies in case a retreat was required. The total force assembled at San Blas numbered a few hundred, and these were mostly Spanish merchants and other elite "peninsulares" or "gachupines" who had fled the rebellion. Most of the townspeople were in favor of the rebels. There were three ships naval present, the San Carlos, Activo, and Concepción, in addition to two merchant ships and a number of smaller vessels. Rebel forces, numbering in the thousands, surrounded San Blas and issued terms for surrender. On November 30, Lavayen and the nine other naval officers met and decided to surrender. Narváez thought the Spanish position was hopeless. The next morning Lavayen capitulated and San Blas fell into rebel hands.
Within a month of the fall of San Blas the revolution suffered a severe defeat near Guadalajara. In the aftermath the royalist army was able to regain control of Tepic and San Blas, among other areas. In February of 1811 Narváez, Lavayen, and nine other officers were brought before a military tribunal, accused on failing to defend San Blas. The officers, including Narváez, were found guilty of treason, but cleared of most of the charges and restored to duty. Narváez continued to serve the Spanish Navy, but made repeated attempts to remove the stain on his reputation.
Narváez, by virtue of being born in Spain, was a member of the elite class known as "peninsulares" or "gachupines". But he had made Mexico his home and became increasingly interested in the general goals of the revolutionary movement, which repeatedly flared up into revolt and violence in various regions. Nevertheless, he remained a royalist and continued to serve the navy. He was put in charge of a voyage to the Philippines and back in 1813-1814.
In 1815 Narváez participated in a blockade of the rebel stronghold of Mescala Island in Lake Chapala, near Guadalajara. Narváez watched as royalist forces attempted and failed to take Mescala Island at least four times, taking significant loses in the process. The Spanish commander in charge of crushing the rebels was Brigadier José de la Cruz, who had also been in charge of the military tribunal that found Narváez guilty of treason in 1811. Having failed to take Mescala Island by storm, Cruz conducted a ruthless scorched earth campaign around the entire lake. Late in 1816 the rebels on Mescala Island finally surrendered.
During 1817 and early 1818 Narváez worked on a project to map the entire province of Jalisco, including charting Lake Chapala. He was also involved in surveying a new road to Guadalajara. On March 20, 1818, he was promoted to alférez de navio in recognition of his service during the Lake Chapala campaign.
By 1818 royalist forces had pacified nearly all of New Spain and the revolutionary movement collapsed. Then in 1821 a young royalist captain, Agustín de Iturbide, formed a partnership with the rebel General Vicente Guerrero, formed a common army and, within the year, marched into Mexico City and proclaimed independence.
In 1822 Narváez was given command of the San Carlos and sailed from San Blas to Baja California and Alta California on a mission to install Mexican commissions and councils in both provinces. By the time he returned to San Blas in March, 1823, Iturbide had been overthrown and a new government set up under Antonio López de Santa Anna. Narváez was appointed Commandant of the Department of San Blas, a position he kept until 1827 when the post was suspended due to funding cuts.
In 1824 and 1825 Narváez was given command of the Mexicana in order to survey and map the coast between the ports of San Blas and Manzanillo. In April of 1825 he was promoted to capitán de fragata. Later that year he produced some maps of the border areas between Louisiana and Texas for the government. In 1826 he became a founding member of an Institute of Science, Literature, and the Arts.
After 1827 Narváez's naval position was eliminated, but he continued to work for the Mexican Navy in various capacities, including the production of a number of maps. He retired in 1831 at the age of 63 and settled in Guadalajara, where he lived on a meager pension. In retirement he continued to make maps, including the first official map of the state of Jalisco.