Rivera entered military service in 1742, serving in Loreto, Baja California, at a time when the colonial settlement of that peninsula comprised mostly Jesuit missions.

He participated in reconnaissance missions to previously unexplored northern areas of the peninsula, together with the Jesuit missionary-explorers Ferdinand Konščak and Wenceslaus Linck.

The story of the Jesuit expulsion is related to European power struggles of the time, but it had the effect of bringing to Baja California three individuals who shaped the subsequent history of the region: José de Gálvez, appointed "visitador" (roughly equivalent to inspector-general, a powerful office reporting directly to the Crown); Gaspar de Portolá, a Spanish soldier from a noble family, and Junípero Serra, newly appointed head of the Franciscan missions.

Portolá, Serra, and Fernando de Rivera were thus together in remote Baja California at the moment when King Carlos III of Spain (advised by Gálvez), concerned about Russian and British encroachment on Spain's Pacific coast claims, ordered an expedition north to settle more northerly areas of The Californias.

After the several land and sea groups reassembled at San Diego (where there was much suffering and death among the sea-borne legs, from scurvy), Rivera continued north with Portolá in the search for Monterey Bay, second objective of the expedition.

Rivera himself was soon in conflict with Serra and the Franciscans, and also with Juan Bautista de Anza, commander of two new overland expeditions to "Alta" California in 1774–75.

The earlier Portolá expedition found San Francisco Bay but, view blocked by the intervening hills, failed to discover its narrow entrance channel.

Also on the 1774 trip, Palóu named a long valley formed (unknown to the explorers) by coastal California's largest earthquake fault, just south of modern San Francisco.

[7] When several Kumeyaay Indian communities joined to sack the mission at San Diego in 1775, governor Rivera had the responsibility of suppressing the revolt.

His final assignment was to recruit settlers for the new pueblo (secular settlement) of Los Ángeles, and transport them to Alta California via the overland route from northern Mexico.

Although the settlers made it safely to southern California, Rivera and many of his soldiers were killed along with the local missionaries including Francisco Garcés, at Mission San Pedro y San Pablo de Bicuñer on the lower Colorado River during the civil resistance uprising and revolt of the Quechan Indians in 1781.

By the time the payments were finally made, Rivera's widow and three of his four children were already dead (though there were also grandchildren, who had suffered in poverty during the interim).