Most pelecaniforms build substantial but untidy nests of twigs, grass, algae, or feathers; in many species, guano accumulates on and around the nest as breeding progresses. Many cormorants and pelicans habitually build their nests on the ground, but most species that normally breed where trees or bushes are available build their nests in them. Certain cormorants and boobies sometimes nest on cliff ledges, and tropic birds and most boobies lay their eggs on the open ground in insignificant depressions.

There is much variation in clutch size. In general, species living in the unproductive tropical seas lay only a single egg. Those living in seasonally productive areas at higher latitudes, or in areas where surface waters are enriched by the upwelling of nutrient laden water from deeper layers, lay larger clutches and raise several young at a time. Tropic birds and frigate birds all have clutches of one egg, but pelicans generally lay one to three eggs, cormorants two to five, and anhingas three to five. The boobies show a more complex picture. The gannet of the temperate zones and the tropical red-footed booby (Sula sula) have clutches of one egg, but the other typical boobies of the tropics—the masked and brown boobies—normally lay two eggs. These two-egg species, however, normally raise only one chick, the older nestling apparently pushing the younger out of the nest soon after hatching. The second egg in these ground-nesting species seems to function as an insurance against infertility, loss, or breakage of the first, risks that may be lower in the tree-nesting red-footed booby. The single-egg clutch of the gannet has not been satisfactorily explained, since pairs have been able to raise two chicks when an extra has been provided experimentally.

Except in the tropic birds, the eggs of pelecaniforms are small in relation to body size. In the tropic birds they are 9–13 percent of the adult weight, in the frigate birds 6 percent, in the boobies 3–5 percent, and in the pelicans and cormorants 2–3 percent. In species with clutches of more than one, eggs are laid at intervals as short as 24 hours or as long as five to six days in the case of the masked booby. In all the groups, both parents participate roughly equally in incubation and feeding of the young. The lengths of the incubation shifts vary extensively, both within and between species. In some species (such as many cormorants) the shifts last only a few hours, but in tropic birds and some boobies shifts of three or more days are not uncommon; in the great frigate bird (Fregata minor), in the Galapagos, shifts last 10–15 days.

Incubation generally starts with the laying of the first egg (though not in some cormorants). First and last young may hatch several days apart and often differ substantially in size during the nestling period. The incubation period is just under four weeks in anhingas, four to four and a half weeks in cormorants, about four and a half weeks in pelicans, six weeks in tropic birds, and six to eight weeks in frigate birds.

The young, which are helpless and essentially naked at hatching, are brooded continuously for several days until their down grows. The tropic birds are exceptional in that they have thick down at hatching and are sometimes left alone by their parents even on the day of hatching. The rate of development of the young varies dramatically and is correlated with the characteristics of the environments in which the birds live. The fledging period in the pelagic tropical masked booby is double that of cormorants of comparable body size living in the cool, productive waters off the coast of North America (17 weeks versus less than 8 weeks). Brown pelicans in North America fledge in less time (9 weeks) than white-tailed tropic birds weighing only one-tenth as much (10 weeks) and in less than half the time needed by tropical frigate birds weighing about one-third as much (more than 20 weeks).

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The young of all pelecaniforms are fed on regurgitated food that they obtain by inserting their heads into the mouths of their parents. In frigate birds and tropical boobies, the parents continue to feed their young for a long period after they can fly, apparently because the young take a long time to become sufficiently skillful in hunting to survive in tropical areas where food is generally scarce. The most extreme case is that of the great frigate bird, in which the young can fly at about five months of age but sometimes are fed for more than a year after this. In the tropic birds and the gannet, however, the young are not fed by the parents after fledging; they leave their birthplace either by flying straight out to sea or by fluttering down to the water and swimming out to sea.