As the climate changes, the effects of agriculture on the environment may change. In the future, an increasing frequency of climate extremes, such as droughts, heat waves, and excess moisture, is expected. Past research on the interaction between environment and resources has focused on climate change effects on various sectors, including agricultural production (especially crop production), but research on the effects of climate change using agri-environmental indicators (AEI) of environmental sustainability of agriculture is limited. The aim of this paper was to begin to address this knowledge gap by exploring the effects of future drought and excess moisture on environmental sustainability of agriculture. Methods included the use of a conceptual framework, literature reviews, and an examination of the climate sensitivities of the AEI models. The AEIs assessed were those for the themes of soil and water quality, and farmland management as developed by Agriculture and Agri-Food Canada. Additional indicators included one for desertification and another for water supply and demand. The study area was the agricultural region of the Canadian Prairie Provinces. We found that the performance of several indicators would likely decrease in a warming climate with more extremes. These indicators with declining performances included risks for soil erosion, soil salinization, desertification, water quality and quantity, and soil contamination. Preliminary trends of other indicators such as farmland management were not clear. AEIs are important tools for measuring climate impacts on the environmental sustainability of agriculture. They also indicate the success of adaptation measures and suggest areas of operational and policy development. Therefore, continued reporting and enhancement of these indicators is recommended.