The most notable one featured three harbours- the Western, Lake, and Great Harbours; it also contained the Pharos and Great Library.
The one Eschate or "the furthest" is now Khujand, Tajikistan. One was located on the confluence of the Kokcha River and a river now known as the Amu Darya but then known as the Oxus. The second and third largest cities in Afghanistan are both modern locations of two of these sites. The best-known one began as a small fishing village called (*) Rhacotis. The one in Aria is now Herat, and the one in Arachosia is now Kandahar, a corruption of its original name.  Two were on the Hydaspes River, one of which was partially named for a horse. The most notable one featured three harbours- the Western, Lake, and Great Harbours; it also contained the Pharos and Great Library. For 10 points, the western end of the Nile River delta had the most famous of which cities founded by and named after the son of King Phillip II, a noted Macedonian conqueror.
The one Eschate or "the furthest" is now Khujand, Tajikistan.
{Alexandria}(s) [accept {settlements founded by Alexander the Great} or reasonable alternatives]