Waterborne transport is widely believed to be one of the most sustainable modes of commercial transportation. However, factors often overlooked such as unmeasured pollution and costs, hazards to crew and general society call into question this particular assessment of the industry. This paper highlights the need for the application of a holistic approach for guiding shipping and related stakeholders towards sustainability using economically viable, less polluting and more human-friendly operating models, and it proposes a structured assessment methodology to achieve it. For it, ships are divided in onboard systems (e.g. propulsion systems, waste generation and ballast water management system) and their sustainability performance is assessed in order to see the ship's whole sustainability index. A definition of sustainable shipping is proposed. There is also a review of the critical pollution, cost and social drivers of ships in operation as well as a discussion about the capabilities and limitations of the current environmental/economical/social assessment tools for quantifying shipping sustainability.