The recent and rapid recession of alpine glaciers over the last 150 years has major implications for associated aquatic communities. Glacial meltwater shapes many of the physical features of high altitude lakes and streams, producing turbid environments with distinctive hydrology patterns relative to nival systems. Over the past decade, numerous studies have investigated the chemical and biological effects of glacial meltwater on freshwater ecosystems. Here, we review these studies across both lake and stream ecosystems. Focusing on alpine regions mainly in the Northern Hemisphere, we present examples of how glacial meltwater can affect habitat by altering physical and chemical features of aquatic ecosystems, and review the subsequent effects on the biological structure and function of lakes and streams. Collectively or separately, these factors can drive the overall distribution, diversity and behavior of primary producers, triggering cascading effects throughout the food web. We conclude by proposing areas for future research, particularly in regions where glaciers are soon projected to disappear.