Two slopes, one gutter
A valley is the inside corner where two roof slopes meet, and everything that falls on both slopes near it ends up running down it. That turns a strip a couple of feet wide into the busiest drain on the roof. Shingles there wear faster than on the open slopes, and small faults that would be harmless elsewhere, a nail a little out of place or a shingle cut a little short, sit directly in the stream.
The usual causes follow from that. Leaves and needles build up and dam the flow, so water backs up sideways under the shingles. In cold weather, ice forms in the valley first and holds meltwater against the roof. Nails driven too close to the center leave holes in the wettest spot on the house. And on older open valleys, the galvanized metal rusts through once its coating has worn away.
Because water follows the deck before it drops, a valley leak usually shows up downhill and to one side of the valley. A ceiling stain near the inside corner where two wings of the house meet is the classic sign.
Which kind of valley you have
Open valleys line the corner with metal and cut the shingles back on both sides, leaving a band of metal showing down the center. Water runs on smooth metal instead of across shingle edges, and debris tends to wash through rather than catch. This is the type the estimate prices: $60 to $110 for a 24-inch galvanized liner, the narrowest the building code allows for an open metal valley (IRC R905.2.8.2), laid over $57 to $95 of self-adhered membrane. Copper or painted steel cost more and outlast galvanized.
In a closed-cut valley no metal shows. Shingles from one slope run straight across the valley and onto the other; shingles from the second slope are laid over them and trimmed in a straight line just short of the center. It is the usual look with architectural shingles. If your valleys are closed-cut, the metal line in the estimate does not apply, but the membrane under the shingles does.
Weaving interlaces shingles from both slopes across the center, alternating like a basket, and suits flat three-tab shingles. The thicker laminated shingles on most newer roofs do not bend into a tight weave, and shingle makers generally call for closed-cut or open valleys with them.
What the rebuild involves
The crew strips the shingles back on both slopes and pulls up the old lining, which exposes the deck. Valleys that have leaked for a while often have soft plywood underneath, and any soft panel has to be replaced, which is priced as decking repair rather than here. Then a 36-inch self-adhered membrane goes down the full length of the valley, bonded to the deck, so water that ever gets past the metal still meets a waterproof layer.
The metal goes on top, fastened only at its outer edges. Shingles are laid back on both slopes with one rule above the rest: no nail near the middle. Shingle makers' instructions generally keep fasteners at least six inches from the center line. The cut ends along the valley are bedded in sealant, $16 to $40 of it, so wind cannot lift them.
Two limits on the estimate. It assumes asphalt shingles; valleys on tile, slate or metal roofs are different jobs with different materials. And fresh shingles in a valley stand out against an older, sun-faded roof for a few years, however close the product.
Spot fix, whole valley, or wait for the new roof
If the leak traces to one cracked shingle or one bad nail and the lining beneath is sound, a roofer can often fix that spot without rebuilding anything. If the lining itself has failed, with rusted metal, perished felt or shingles worn thin along the whole run, patching one spot moves the leak a few feet downhill. That calls for the full valley, ridge to eave.
Timing matters too. Every roof replacement rebuilds the valleys as a matter of course, so on a roof with only a few years left, a full valley now is money spent twice; a holding repair may be enough. Line up competing quotes against three things: the valley type named, a full-length self-adhered membrane, and, for an open valley, new metal. A "valley repair" that mentions none of those may be new shingles over the old lining. The roof flashing guide explains valley metal alongside the other flashing a roofer may quote.