They operate in either directions simultaneously. So you can opt to either of the routes. That is Kollam to Alappuzha or Alappuzha to Kollam.
Earlier this was a very popular commuter route operated by the state water transportation department. But the same distance by road (that runs almost parallel to the waterway) connects Kollam with Alappuzha in udder 2 hours (85km). For obvious reasons this public ferry was cancelled some years back. Now the route is very popular among the tourists, and operated by the district tourism.
The cruise starts at 10.30am at both Alappuzha & Kollam and ends by 6.30pm. You can buy tickets directly at the DTPC (District Tourism Promotion Council) office located next to the boat jetty in Kollam (near the KSRTC Bus stand) and boat jetty in Alappuzha. Get to the ferry point at least 30min prior. Also remember the December-January peak season can see the tickets getting sold out quick. Ticket cost Rs300 per head.
Carry snacks and beverages. You can also buy from a limited choices available on-board. The journey include two breaks : a 45 min lunch break at Alum Kadavu (by 1pm) and a tea break at Thottapally.
The boat journey essentially connects three large backwaters of Kerala , Vembanad, Kayamkulam and Ashtamudi lakes by a canal system.
You can chose to return by the same boat, the next day or even catch the bus from the nearby KSRTC bus stand. Also remember the boat halts at many jetties on the way.
Alappuzha to Kollam itinerary: Alappuzha --> Kannitta --> Pallathuruthy --> Kanjipadam --> Thottappally --> Thrikkunnapuzha --> Ayiramthengu --> Amritapuri --> Chavara --> Kollam
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The pomp and fanfare apart, touring backwaters of Kerala in houseboat is an expensive affair. The rates are usually steep, running into a couple of thousand rupees per night, even during the off season.