Increasing attention is being paid to the ecological consequences of underwater noise generated by human activities such as shipping and maritime industries including, but not limited to, oil and gas exploration and extraction, sonar systems, dredging and the construction of offshore renewable energy devices. There is particular concern over the extension of these activities into previously undeveloped areas of the oceans, including Polar Regions and areas of coral reef habitat. Most of the concern by regulators and others has focussed upon effects upon marine mammals and other protected species. However, examining the impacts upon the overall ecology of affected habitats is also important as it may be dominated by effects upon the far larger biomasses of fishes and invertebrates, which do not have the same degree of legal protection. Many of these assessments of the impact of noise on fishes and invertebrates have overlooked important issues, including the sensitivity of a substantial proportion of these species to particle motion rather than sound pressure. Attempts have been made to establish sound exposure criteria setting regulatory limits to the levels of noise in terms of effects upon mortality levels, injury to tissues, hearing abilities, behaviour, and physiology. However, such criteria have almost exclusively been developed for marine mammals. Criteria for fishes and invertebrates have often had to be assumed, or they have been derived from poorly designed and controlled studies. Moreover, the metrics employed to describe sounds from different sources have often been inappropriate, especially for fishes, and invertebrates, as they have been based on sound pressure rather than particle motion. In addition, the sound propagation models employed to assess the distances over which effects might occur have seldom been validated by actual measurements and are especially poor at dealing with transmission under shallow water conditions, close to or within the seabed, or at the surface. Finally, impacts on fish and invertebrate populations are often unknown and remain unassessed. This paper considers the problems of assessing the impact of noise upon fishes and invertebrates and the assessment procedures that need to be implemented to protect these animals and the marine ecosystems of which they form an integral part. The paper also suggests directions for future research and planning that, if implemented, will provide for a far better scientific and regulatory basis for dealing with effects of noise on aquatic life.