Below are quotes from a thread found in the Amtrak Rail Discussion forum: Silver Star - WAS - JAX. The information seemed well suited to the What to See, and Where? forum, especially since there was no prior thread related to Jacksonville.
Regarding the JAX station, it is far enough from downtown that an automobile is needed to get around. Taxis are plentiful at the station as well as city bus service. No rental car counters but I have seen Enterprise pick up/drop off passengers so that is an option.
JTA buses leave and return from the Amtrak Station every 35 min on weekday, every hour or so on Saturday and every 90 minutes on Sunday and holidays. The K7 route goes downtown and then directly to Jacksonville Beach. Its about 25 minutes to downtown JAX and 90 min to the beach.
The most interesting place downtown is Jacksonville Landing by the St. John's River which has restaurants, some shops and entertainment at times. There is a water taxi downtown that goes to various points on the north and southside of the river. Unfortunately, no public transportation from Jacksonville to St. Augustine, but that may change whenever service on the FEC line begins. As the previous poster pointed out, you really need a car to see the sights as JAX is not a transit friendly city.
To add to an accurate, good, and informative description from jphjaxfl, once you get to Downtown Jax there are riverwalks along both the Northbank (the Downtown side where the Jacksonville Landing festival marketplace is) as well as along the Southbank, via the aforementioned water taxi or the Skyway automated transit system.
Strolling along either riverwalk, you should be able to see seabirds and dolphins in the river - and maybe even a manatee or two.
There are nice restaurants and hotels along the Southbank. There you will also find Treaty Oak Park, Friendship Fountain, and the decent Jacksonville Museum of Science & History (MOSH).
If you find yourself out at the Beaches (Jax, Atlantic, or Neptune) there are, in addition to the beautiful beaches, plenty of restaurants, bars, shopping, etc. - more so at Neptune Beach or Jax Beach instead of Atlantic Beach, which is mostly residential.
If you have access to a car, St. Augustine, the Fernandina Beach waterfront, and the intown neighborhoods of San Marco (south of the river) and Five Points/Riverside/Avondale (west of the river) are all excellent bets. Don't overlook the Cummer Museum of Art & Gardens if you are in the Riverside area. It alone is worth the quick taxi ride from Downtown.
Enjoy your visit to our First Coast!
Jacksonville's former (and future?) Amtrak station, the old Union Terminal is on the west side of downtown. It is now part of the Osborne Convention Center, though there were (maybe still are?) plans to return the old terminal to its original use as a passenger rail station.
Anyway, it's worth getting a glimpse of it if you're a fan of railway architecture or history. Listed with the National Register of Historic Places, the passenger terminal opened in 1919 and serviced trains for FEC, ACL, SAL, Southern, and GA Southern & FL, and later their successors until its last, lone tenant, Amtrak left in 1974. The building is not hard to spot, known by a distinctive front facade which features a row of massive columns beneath three identical peaks, side-by-side, which define its roof. Train tracks still pass in the distance to the south of the building.
In relation to Jacksonville Landing, the Convention Center/ex-Union Terminal is directly to the west about nine city blocks, at the opposite end of Water Street. If you're there during the week, you can ride the free JTA Skyway to the Convention Center. You'll pass the west-facing "Jacksonville Terminal" building on your way to the Skyway station, which sits just north of the Convention Center.
And if you do decide to go check the Terminal out, an excellent suggestion in my opinion, then don't overlook semi-preserved Atlantic Coast Line steam passenger locomotive 1504, a P-5 USRA design Pacific type. She's sitting quietly in the parking lot behind the building.
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