The John Muir Trail is a popular trail through the national parks of Yosemite, Kings Canyon, and Sequoia. Most of the route lies in the High Sierra backcountry through high mountain scenery. As such, it sees very remote wilderness, and very high elevations. In part due to the significant elevation change and high altitudes, the trail is considered quite strenuous. On other trails this relatively short distance might be completed in under two weeks, but the JMT typically takes around three weeks or longer to complete a full thru-hike. Most hikers will hike north to south, in order to allow for more gradual acclimation to the environment.
The route meanders through the Sierra Nevada mountain range, where the terrain consists of high rocky mountains with sharp switchbacks, but also other primary features of remote wilderness with dense forests and many lakes and creeks throughout. The high altitudes and rapid changes in elevation (along with the rocky, mountainous environment) makes for difficult terrain. It's important to start off slowly and ensure that you gradually adapt to the increasing difficulty.
Water sources along the JMT are generally plentiful, from both natural creeks as well as occasional sources in developed areas like campsites. However, as with many areas of the California, availability of water varies significantly by year. In some very dry years, it is certainly possible that more thorough planning would be required to ensure that there would be enough water for hiking. In any case, it is recommended to bring some type of water filtration system. On the plus side, the natural water in the High Sierras tastes great.
Since the trail passes through National Parks, you can often use developed areas in the parks as resupply points. If you plan ahead properly, you should be able to space out your resupply packages across 4-5 points, which means you would need to carry several days worth of food (up to 10 days depending on the stretch). Many hikers will mail resupply packages to points ahead of time, and some will make other arrangements to have friends bring supplies at other points along the route.
The early parts of the season may still have snow on the ground in many areas, especially near the higher mountain passes. During the primary hiking season, the weather generally remains pleasant with sunny, dry days, and cool nights. As with most trails, hikers still need to be alert for severe weather. Short thunderstorms in the afternoons are not uncommon, but more severe dangerous storms are quite rare.
Navigation on the John Muir Trail is typically straightforward, as this is a very famous and well-travelled trail. However, hikers are still encouraged to bring some form of map (paper or digital GPS) and guidebook for safer hiking. There are several popular guidebooks available which condense trail information and navigational mapping. These are often considered indispensable for proper planning, especially with some of the logistical necessities for resupplying.
The primary risks lie in the dangers of snowy and icy terrain towards the beginning of the season. Icy slopes and storms could be very dangerous in the mountain passes. These risks diminish significantly as the season progresses, and the snow and ice melts away. During the main hiking season, there are some mild dangers associated with traveling in high altitudes across much of the route. There are bears in this region, so all food will need to be kept in a bear canister. Severe weather remains a danger, but with proper rain gear and dry clothing, this will not pose a significant threat.
The JMT is famous around the world, and is one of the most popular long distance hiking trails in North America. During the primary hiking season, there will be an average of several dozen hikers per day on the trail - most attempting a thru-hike. Because of the high popularity, there is a quota of hiking permits (most of which are reserved in advance), with new availability each to day to spread out the large numbers of hikers.
If you live in the area and can drive, there are long-term parking options at both ends of the trail. In this case you can park on both ends with multiple cars, or park on one end and use public transportation at the terminus. The bus system is not complete, but can get you close to various trailheads using a combination of YARTS, Eastern Sierra Transit, and local Yosemite buses. Many hikers will opt for private shuttles, which are expensive, but are the most direct route to the trailheads.
Most hikers will use some form of tent or tarp for personal shelter. Hammocks are doable as well, but harder to setup on portions of the trail that are above the tree line. As much of the John Muir Trail passes through remote wilderness, there are not many options for developed accommodation. The exceptions are occasional grounds around national parks that have more developed access to running water and electricity.