The development of inland waterway transport is growing. The Melaka River, located in the historical city of Malacca, Malaysia, was once utterly filthy. However, after upgrading and beautifying the river, it has become attractive. Melaka River Cruise has become one of the tourist attractions in Melaka. Nevertheless, with the rapid increase of boats navigation, environmental sustainability will also decline. Therefore, a study on the pollution resulting from the boat navigation and also the level of pollution caused by boats navigation in the Malacca River is necessary. The data were collected from the enforcement of the Malacca River, Jabatan Pengairan dan Saliran (Drainage and Waterways Department), Melaka and also from the authorities of the Melaka River Cruise River, which is Perbadanan Pembangunan Sungai dan Pantai (River and Beach Development Authority), Melaka. Results from this study will help the authorities to minimize contamination of the Malacca River by from the boat. This study also provides recommendations that can be used in addressing the solution of pollution resulting from the use of boats.