In certain alpine systems, glacially‐fed lakes and streams have nitrate concentrations one to two orders of magnitude higher than lakes and streams fed by snowmelt alone. To better understand how nitrogen subsidies from glacial meltwater propagate down a chain of lakes and streams we assessed the effects of these subsidies in a set of aquatic chains in the central U.S. Rocky Mountains. Algal biomass, algal community assemblage, and nutrient limitation were measured in a chain of lakes and streams fed by glacial meltwater (GSF) and a chain fed by snowmelt alone (SF). Nitrate ( NO3–) concentrations in the GSF chain ranged from 228 to 70 μg L−1 declining from the top of the chain to the bottom, while NO3– concentrations in the SF chain were consistently low, < 9 μg L−1. In the glacial chain, both lakes were phosphorus‐limited; the strength of this limitation signal weakened down the chain, with the lake at the bottom showing secondary nitrogen and phosphorus colimitation. In the snowmelt chain, lakes were colimited with no change in strength down the chain. Algal biomass averaged 2.6 μg L−1 and 7.3 μg m−2 in SF lakes and streams and 5.4 μg L−1 and 9.2 μg m−2 in GSF lakes and streams. Phytoplankton and periphyton communities in the GSF chain were more homogeneous compared to the SF chain. Our results indicate nutrient subsidies in glacial meltwaters can propagate down aquatic chains and alter nutrient limitation patterns and algal communities compared to SF systems, creating heterogeneous patterns across the landscape.