Experience demonstrates that none of the available measures regarding biological effects of pollution can be considered ideal, which is due to the complexity inherent in assessing the environmental quality of a system. In fact, it is always preferable to combine a suite of indices providing complementary information. This book aims at helping researchers and students, as well as managers and authorities of coastal areas in selecting the most suitable ecological indicators for each case, taking into account the type of disturbance they want to assess and the data available to do it. A user friendly guide is proposed, accounting different theoretical approaches and discussing the results of its application in different geographical areas. Recommendations are provided regarding the most adequate application of different indices, illustrating for instance in what situations their use is recommendable, or on the contrary not advisable, depending on the characteristics of the disturbance, the type of data, or the level of taxonomic identification of the organisms.