Some specific geographic headcanon guidelines for the Downfall Timeline include…
Kokiri Forest – The forest actually suffered a lot of infrastructure damage from monster attacks, and the trees were barren for quite some time. Fortunately, the establishment of contact between the resident Kokiri and the outside world, following the sealing of Ganon and the Triforce, means that there is plenty of help to be had rebuilding child-sized infrastructure and removing monsters. The trees have begun to recover as well, bearing more and larger fruit and regaining their green foliage.
Lost Woods – More sinister and winding than ever before. The very trees and branches seem to reach out, now, trying to snag and strangle any visitors, Kokiri or otherwise, who dare to enter. Even the resident Skull Kids are beginning to feel the labyrinth’s wrath, with many emerging from the dense thickets, and taking shelter with the Kokiri instead. It is highly recommended that one does not enter, unless they are in the company of one of the Sages, or another particularly powerful magic-user.
Death Mountain – Nearly erupted under Volvagia’s onslaught, but fortunately, Link. Still, many smaller magma plumes breached the surface during the battle, so the topography of the area has changed a lot. It’s not dangerous anymore, but it is different.
Goron City – Some of those magma plumes burst out and flowed through the city; not so much a problem for lava-proof Gorons. More for their Bomb Flower crops, which, err… there were a lot of rockfalls. The city is in rough shape in more of a topographical sense; new rock formations caused by lava flowing through the city, fallen rock from the cavern roofs, etc. The Gorons, fortunately, ever resilient and cheery people, can see the silver lining of this, and are working to turn the new features into helpful or fun things.
Dodongo’s Cavern – Much the same as Goron City; there are new structures here, caused by pyroclastic flows and rockfalls, but it’s largely unchanged, and the creatures making their home there don’t seem to mind the new topography much.
Zora’s River – The flash-flooding common to the river due to rapid, erratic snow and ice melt in Zora’s Fountain is beginning to taper off, with the Domain and Fountain thawed and no longer freezing over. The ecosystem has shifted toward something more lotic than lentic, with monsters such as aquatic Deku Babas taking over from the free-floating Octoroks that had previously been buzzing about in the slower flow.
Zora’s Domain – Still recovering from being frozen; a lot of the wildlife was not happy with the drop in temperature, so the Zoras are finding themselves having to basically rewire the ecosystem from Step One. Fortunately, Lakeside Laboratory’s Professor is quite knowledgeable when it comes to aquatic species, and is helping to kick-start the process. The rocks have been broken in some places by the freezing water that seeped into them, but physical damages were kept to a minimum by the nature of the area.
Zora’s Fountain – Also recovering from very cold temperatures. Many of the same problems as the Domain, as well as fewer pulsed water events; the Fountain no longer freezes and thaws in unpredictable cycles, rendering Gerudo Valley and Zora’s River less prone to flash-flooding than they have been.
Lake Hylia – Remains largely unchanged, thank goodness. The lake is still full of clear, pure water, and now that the level has returned to normal, it’s a good reservoir for the thirsty populace.
Gerudo Valley – The bridge has been rebuilt, and the transport of supplies to the Fortress can now continue. It’s a nice change, being able to get wagons across again; the bucket-and-pulley system previously used did not work so well. The gorge is also less prone to flash-flooding now that Zora’s Fountain has stopped the rapid freeze-thaw cycle started by warring magical energies.
Haunted Wasteland – Not much has changed in terms of climate and harshness, but it is, like the rest of Hyrule, subject to more frequent monster. The main focus for the Gerudo, and any other defenders who choose to step into the fray, is preventing the larger, more dangerous creatures, such as venomous or fire-breathing beasts, from reaching the Fortress and wreaking havoc.
Castle Town Ruins – Battered and smashed from the final battle between the three wielders of the Triforce, Castle Town and Hyrule Castle itself have suffered quite a lot of damage over the seven-year time period, especially after the rampage of an enhanced Ganon, powered by the entirety of the Triforce. Now blighted by dark magic, and haunted by monsters, mainly undead, the Ruins show no sign of recovery from the choking miasma of death and corruption that covers them, even after several years, and several fruitless applications of purifying Light Magic. The exception is the Temple of Time, which remains both standing, albeit battered, and pure. It serves as a temporary refuge to those trapped in the ruins. The entrance to the Sacred Realm, now the Dark World, is also located here. Zelda has declared the ruins off-limits, unless one is in the company of either herself, or one of the surviving Sheikah.
The reason for the Castle Town Ruins’ continuing corruption and the continued presence of monsters is the energy leaking from the Dark World, which has its entrance in the Temple of Time. It’s not noticeable at first; the Master Sword projects such a strong aura of light as to make it virtually undetectable. But Ganon whispers from his prison inside, the greedy and weak-willed listen, they reach the Dark World, and they are transformed into monsters. The entrance won’t be fully sealed until the Imprisoning War that precedes A Link to the Past. I sorta combined and squished up the backstories a little bit to make it work with both OoT and ALTTP’s canons.
This is currently a secret to everyone in-universe.
Kakariko Village – The new center of Hylian civilization given the state of Castle Town, and the lack of resources to rebuild it, currently. Kakariko still has a fairly small-town atmosphere, but is well on its way to becoming the big city that Impa hired the carpenters to build it into. Zelda currently maintains a residence, here, though she’s rarely actually there. A wall has been built near the entrance to the village proper, and the agricultural fields lie just beyond, easily defensible by the village’s inhabitants. Most residents also tend to avoid the Graveyard during night hours. It’s more of an unwritten rule than an actual edict, though.
Lon Lon Ranch – Also subject to protection by Kakariko’s defenders, given its importance as a food source and in raising horses and other beasts of burden. Also subject to more frequent monster attacks, but between the contribution from Kakariko, and the fed-up ranch residents’ eagerness to strike back against the beasts, it’s… not too much of a problem, generally. Again, the main concern is monsters with additional powers, such as elemental control, or poison.
If your character is tied to one of these areas, and you have some different ideas, then by all means, hit me up! My purpose here is to spur thought as to how your muses would fit into this post-tragedy world I’ve got cranking in my brain, and if you have ideas, I want to hear them!