Assessment of ecological changes relative to disturbance, either natural or human-induced, confronts a fundamental problem. Ecosystems are complex, variable, and diverse in nature; consequently, the need for simplification to essential features that would characterize ecosystems adequately is generally acknowledged. Yet there is no firm prescription for what to measure in order to describe the response and recovery of ecosystems to stress. Initial focus is provided by identifying relevant ecological endpoints, i.e., ecological changes of particular relevance to humans. Furthermore, we suggest generic purposes and criteria to be considered in making choices of ecological indicators that relate to those endpoints. Suites of indicators, with variety of purposes, are required to assess response and recovery of most ecosystems and most stresses. We suggest that measures of certain ecosystem processes may provide special insight on the early stages of recovery; the use of functional indicators as complimentary to other biotic indicators is highlighted in an extended example for lotic ecosystems.