Climate change and variability will increasingly affect aquatic ecosystems in addition to existing stressors. Bioassessment programs use bioindicators to measure ecosystem condition, generally focusing on changes caused by land alteration or pollution. Climate change, however, will shift the baseline condition at all sites, including impaired and non-impaired. Therefore, managers in bioassessment programs that use a reference condition approach to determine impairment will need to be able to distinguish climate change effects from others. We reviewed available literature on climate change effects on aquatic ecosystems and developed a framework that categorizes indicators according to their responsiveness to climatic changes versus other stressors. The most responsive bioindicators may be able to detect effects of climate change, particularly when monitoring data are compared across impaired and non-impaired sites, while the least responsive may be used to identify other stressors. We distinguish five classes of responsive bioindicators: (1) phenology, (2) number of reproductive periods, (3) climate-sensitive life stage, (4) thermal tolerance, and (5) hydrological tolerance. We used these classes to categorize indicators for phytoplankton, macroinvertebrates, fish, and plants. For example, changes in emergence dates of mayflies might indicate climate change effects, if they occurred across a range of conditions in a given region.