There are tours that leave Chania via bus on the Omolos Road and drop you off at the head of the gorge. I am not sure if any guides accompany you through the gorge; that might depend on the tour you choose. The hike of approximately 16 km takes an average of 4 -7 hours, depending on your fitness and the number of stops you make. When you reach the end, the village of Agia Roumeli, you’ll definitely want to have a swim and something to eat at the seaside tavernas. The tour includes a ferry ride from Agia Roumeli to Sfakia; where the bus meets you for the ride back to Chania. This is definitely a full day excursion, but well worth it.
If you want to do a shorter hike, you can take a bus or your rental car to Sfakia, Sougia, or Paleochora and take the early morning ferry to Agia Roumeli. Some people hike the gorge from the sea to the Iron Gates; a much shorter distance….but remember that you’d have to double-back to catch your return ferry from Agia Roumeli.
If you do either day trip by yourself, just be sure to research the bus/ferry schedules ahead of time so that you don’t get caught over-night in Agia Roumeli (though I can think of worse problems - it would be beautiful!)