Found in flat topographical areas (Nicholson 1997) with moist to wet woods (Fussell 1994), in swamps (especially cypress) and along heavily wooded streams (Potter et al. 1980). Water is almost always present in the form of pools, ponds, or other slow-moving bodies (Dunn and Garrett 1997).

Builds nest inside a cavity of a tree, inside a stump, in the hollowed top of a broken tree (Pearson 1959), or in a cypress knee (Nicholson 1997). Will do some excavation in rotten stumps (Ehrlich et al. 1988). Often uses old woodpecker holes, particularly those of the Downy Woodpecker (Griscom and Sprunt 1957). Will also use nest boxes (Ehrlich et al. 1988) and bird houses, or occasionally nest in sheltered places such as under bridges or in boat houses (Griscom and Sprunt 1957). The nest cavity is often located over water (Ehrlich et al. 1988), but may be far from it (Dunn and Garrett 1997), although those far from water may be in easily flooded areas (Griscom and Sprunt 1957). The cavity is usually less than 6 feet from the ground but may be over 25 feet (Dunn and Garrett 1997). Gleans the foliage of reeds, bushes, limbs overhanging streams (Pearson 1959), rotten logs, and around the edges of water (Dunn and Garrett 1997).

NATURE SERVE GLOBAL HABITAT COMMENTS:

BREEDING: Mature deciduous floodplain, river, and swamp forests; wet lowland forest. Primary habitats are almost always near standing water; swamps that are somewhat open with scattered dead stumps are preferred. Bottomland forests and extensive willow thickets near lakes or ponds are also quite suitable. Requires dense underbrush along streambanks (Bushman and Therres 1988). Nests in cavity (natural, old woodpecker hole, bird box, etc.), in snag or living tree, often or always near or over water, at average height of 1.5-3 m (range 0.9-9.8 m); male selects territory, nest site, places some material before female's spring arrival. May be limited by the number of available nesting cavities. See Blem and Blem (1994) for information on composition and microclimate of nests in Virginia. This is the only eastern warbler that nests in tree cavities or other crannies (the only other cavity-nesting wood warbler (Parulidae) is Lucy's warbler [VERMIVORA LUCIAE]). Petit and Petit (1988) provided the first record of a prothonotary warbler using an open-cup nest built by another species (red-winged blackbird [AGELAIUS PHOENICEUS]).

Hamel et al. (1982) provided details on habitat use and suitability in Virginia, North Carolina, South Carolina, Georgia, and Florida. The following five vegetation types used by this species in five physiographic provinces (Piedmont, Sandhills, Inner Coastal Plain, Outer Coastal Plain, and Coastline) are listed in order of decreasing suitability: oak-gum-cypress is suitable at the sapling-poletimber successional stage, but optimal at the late successional sawtimber stage; both bay swamp-pocosin and elm-ash-cottonwood are only marginal at the sapling-poletimber stage and suitable at the sawtimber stage; southern mixed mesic hardwoods are only marginal in both the sapling-poletimber and sawtimber stages; and pond-pine pocosin is marginal at the late successional sawtimber stage only. In all cases, shrubs, midstory canopy and dead trees or limbs are used for all activities (foraging, nesting, perching, roosting, and singing), and snags must have a dbh of at least 15 cm.

Kahl et al. (1985) described habitat around song perches in Missouri as typically level terrain, with a small number of woody stems (< 2.5 cm dbh; < 2800 per ha, never > 4200), short ground vegetation (< 0.20 m, never > 0.36), and a high canopy (16-40 m, never < 12). Other important features included few dead stems (2.5-9.9 cm dbh; < 200 per ha, never > 250) and an intermediate subcanopy closure (30-80%, never < 10 or > 90).