Each of the bioindicators identified here has a different response time (i.e. from near instantaneous to years) and specificity to changes in water quality, and the final choice of bioindicators must depend on the specific objective and timeframe available for a monitoring programme. Responses that are specific to disturbances such as nutrient availability, sedimentation and turbidity and that demonstrate a rapid response time, can provide an early warning of changes in water quality. In particular, sublethal bioindicators that reflect rapid changes at the genetic/colony level of selected species may be among the most effective ways to pre-empt mortality of corals and impacts to the wider community. In addition, understanding the processes acting within colonies and among the life-history stages of a selected species will provide a better understanding of the consequences of changes in water quality on populations and coral-reef communities. The comparison of responses from a composite of bioindicators will provide the most useful information on the status and trends of reef ecosystems. As the extent of water-quality degradation increases, so does the scale at which the responses are manifested, and the time taken for the system to return to its previous state when the stressors are removed. Responses to small changes in water quality may be best measured by focusing on rapid sublethal effects at the genetic/colony level in the most susceptible species or life stages; when the stressors are removed, then the condition of these organisms may rapidly return to their previous state. With further decreases in water quality, responses will be measured as partial mortality or mortality of organisms in an increasing number of species or life stages, which becomes evident at the scale of populations and communities, and these signals will remain measurable for months to years after the stressors are removed. Finally, extreme decreases in water quality produce widespread mortality across a range of organisms that will be evident at the level of entire communities and as a shift in ecosystem state; the time taken for the response to be manifest will vary between chronic or acute events, but recovery, when the stressors are removed, is likely to occur slowly. This is best conceptualised when the bioindicators are represented against increasing levels of stressors, from sublethal stress to mortality (Fig. 2). Exposure to a low-level stress will first invoke a response at the genetic and colony level, such as symbiont photophysiology and coral brightness. As stress increases, either in terms of duration or intensity, responses at the population and community level may become evident through reduced juvenile densities, changes in the community structure, through the loss of susceptible species, increased macroalgal abundances, reduced abundances of large symbiont-bearing foraminifera, and a reduction in the maximum depth of coral-reef development. Response time is, therefore, a critical criterion that underpins bioindicator selection in any environmental monitoring. Moreover, exposure to changes in water quality may invoke different responses in some groups, e.g. elevated nutrient concentrations and turbidity decreases coral brightness, while sedimentation stress increases brightness (through bleaching) on upward facing surfaces. Hence, important information on the specific forms of stress can be gained by investigating the direction and magnitude of responses relative to reference conditions.