There are daily ferries going into Malaysia from Singapore into the state of Johor and cruise ships going to other parts of Malaysia. Its a good option to travel by sea if you want to go to the eastern part of Johor, such as Desaru. Ferry terminals in Singapore are at: HarbourFront, Tanah Merah, Pasir Panjang (domestic), Changi Point Ferry Terminal, Changi Ferry Terminal.

There are daily ferries going into Malaysia from Singapore into the state of Johor. Its a good option if you want to go to the eastern part of Johor, such as Desaru.

Ferry from Singapore to Malaysia

Tanah Merah Ferry Terminal (Singapore) to JB International Ferry Terminal (Johor Bahru) & Sebana Cove (Johor); and Harbourfront terminal to Sebana Cove.

Changi Ferry Terminal (near hawker centre) to Tanjung Belungkor (Johor) and Changi Point Ferry Terminal to Penggerang (south east Johor).

Cruise Ships from  Singapore to Malaysia

Cruise ships stop at: Singapore Cruise Centre, HarbourFront Centre, 1 Maritime Square #01-18, Telok Blangah Road. Cruise ships stops mainly at Penang Island, Porto Malai on Langkawi Island and Port Klang in West Malaysia and Kuching, East Malaysia.

Details on ferry and cruise ships in Singapore at (external link):

........Singapore Maritime Portal

........Singapore Cruise Centre

If you have not found what you are looking for, try these:

• Getting to Malaysia
• Air transport in Asia
• Free hotel comparison tool, to compare 30 prominent booking sites  -  HotelsCombined.com