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Mountain glaciers are retreating rapidly due to climate change, leading to the formation of downstream lakes. However, little is known about the physical and biogeochemical conditions in these lakes across a range of glacial influence. We surveyed alpine lakes fed by both glacial and snowpack meltwaters and those fed by snowpack alone to compare nutrient concentrations, stoichiometry, water clarity, chlorophyll, and zooplankton communities. Total phosphorus (TP) and soluble reactive phosphorus were two times higher in glacial lakes than in non‐glacial lakes, while nitrate concentrations were three times higher. However, organic carbon concentrations in glacial lakes were two times lower than in non‐glacial lakes. The carbon‐to‐phosphorus ratio and the nitrogen‐to‐phosphorus ratio of lake seston increased with water clarity in glacial lakes, suggesting that turbidity from glacial flour increases light limitation and increases stoichiometric food quality for zooplankton in newly formed lakes. However, chlorophyll aconcentrations did not differ between lake types. Through structural equation modeling, we found that glaciers exhibit a bidirectional association with nitrate and TP concentrations, perhaps mediated through landscape vegetation and lake clarity. Zooplankton communities in high‐turbidity glacial lakes were largely composed of cyclopoid copepods and rotifers (i.e., non‐filter feeders), while non‐glacial lakes tended to be dominated by calanoid copepods and cladocerans (i.e., filter feeders). Our results show that glacier‐influenced lakes have biogeochemical and ecological characteristics distinct from snow‐fed mountain lakes. Sustained studies are needed to assess the dynamics of these unique features as the influence of the alpine cryosphere fades under ongoing climate change.