This article aims to review 1) the major and most frequent human-induced physical disturbances and their consequences on coral reef habitats using a multi-scale approach, and 2) the scale-related indicators and conceptual aspects used to detect and measure the effects of these physical impacts. By physical disturbances, we mean direct perturbations that lead to the destruction/erosion of the carbonate framework. Human-induced direct physical disturbances are numerous from coastal development, tourism, harvesting, accidents and nuclear/weapon testing. Since methods for monitoring and measuring indicators are generally scale-implicit, coral reefs are first presented according to different ecological-spatial scales of organization, from colony to region (colony, reefscape, reef zone, whole reef, island and region). In this way, it is easier to link a couple {habitat, disturbance} to their potential indicators and to the descriptors they target. Three classes of descriptors, related to the response of the living component of coral reef ecosystem, are considered here: stony coral, reef fishes and the human uses. A synthesis of the different options for coral habitat assessments is proposed. We sort them according to their objectives (monitor, initial status or improvement of knowledge), their specificities (identification or not of a specific disturbances) and their scale of investigation (small, meso- or large scales). Usually, the majority of the indicators of human-induced disturbances are non-specific. They reveal that something is happening but not the actual causality and can only detect differences across time or space. A major weakness lies in the difficulty in deconvoluting the signals from a conjunction of stressors occurring at different scales. As such, a hierarchical concept of disturbances in coral reefs would be the next logical step to enhance our capabilities in monitoring and forecasting coral reefs status.