Hi,
Due to the time of transfer, a trip in Mekong to Phnom Penh normally takes 3 days/2 night. I suggest you here an itinerary for you.
Day 1: Ho Chi Minh-My Tho city – Ben Tre province – Can Tho city

• 07.45 am, Discovey Indochina tour guide and driver pick you up on request at your hotel 
• At 08.00am, leave Ho Chi Minh city. It takes one hour and thirty minutes driving to get to My Tho town. One the way, travellers will have chance to see these beautiful landscape along the road such as the green rice fields, the peaceful Vam Co Dong river and the busy Long An town. En route, Our bus will stop at Mekong rest stop where you can take a rest and see bonsai garden.
• Arrive to My Tho town, visit Vinh Trang pagoda an oldest ancient one in Southern Vietnam. 
• After passing Rach Mieu bridge, we disembark at Thoi Son Islet that locates on Phoenix Island. T
• Then visit honey bee farm and taste delicious honey tea with lemon that is really good for health. Local people also have python farm for those tourist, who like adventure can take a photo with pythons.
• Then cruising to Unicorn Island to visit crocodile farm and visit the remains of Coconut belief.
• Having lunch in orchard garden. Do not forget to taste dried Ear Elephant fish that is one of the special dishes in Mekong Delta (on guest’s account)
• Then take a short walking through the narrow village path to the bus and process to Can Tho city.
• Arrive to Can Tho city
• Leisure in the evening for exploring Tay Do night market, Ninh Kieu wharf or taste these delicious local dishes.

Day 2: Can Tho city – Cai Rang floating market – Chau Doc

• After breakfast at the hotel. At 07.00am, take a leisurely waking to Ninh Kieu wharf. Tourist will have chance to see morning streets market with many products homemade such as fruits, vegetables, cake… are sold on the way to the wharf.
• Cruising in the river to the busy Cai Rang floating market, one of the biggest floating market in Southern Vietnam. Visitors will be surprised to explore “the method of the business” in the floating market areas. It is really impressed.
• After exploring the floating market, visitors will visit the place to see how they make rice vermicelli noodle and the orchard garden. Wandering in the village and  try your best to cross the bamboo bridge which is built only one bamboo tree.
• Cruise back Ninh Kieu wharf.
• After having lunch, process to Chau Doc.
• Arrive to Chau Doc town, visit Sam mountain and Cave pagoda.
• Check in the hotel and leisure in the evening.

Day 3: Chau Doc – Phnom Penh (B) 

• After breakfast. Transfer to the ferry for boarding the speed boat to PhnomPenh.
• Arrive in Phnom Penh around 2.00 pm at the Sisowath tourist dock

For more information, you can email me [email protected] or visit http://www.discoveryindochina.com/cruise/lecochinchine-cruise