Acid mine drainage (AMD) is a legacy left behind by abandoned and active mines that affects all environmental media. Contamination of water resources by AMD presents significant challenges to aquatic ecosystem stability and on the abundance and diversity of aquatic species. Aquatic organisms react and are affected differently by these conditions. Several studies have reported on how AMD affects aquatic organisms with most of these studies focusing on a specific group of organisms or characteristic of the water. This review paper presents a holistic view on how aquatic organisms cope with, and are affected by the high acidity, high heavy metals content and precipitation of oxides of iron and aluminium which are characteristic of AMD contaminated freshwater ecosystems. Mechanisms of tolerance and the effects of high acidity, high heavy metals content, and precipitates of oxides of iron and aluminium on diatoms, algae, fish, and amphibians are discussed. The paper concludes by discussing the implications of AMD contamination of aquatic environments on the United Nations Sustainable Development Goals (SDGs) and recommendations on possible future prospects.