We investigated meso-zooplankton nutrient recycling as a driver of nitrogen deficiency for phytoplankton production in Arctic Alaskan lakes. Copepods and cladocerans differentially recycle inorganic nutrients based on nutrient demands for new tissue. Copepods typically sequester more nitrogen in the tissue, and can lead to nitrogen, relative to phosphorus, deficient conditions for primary production. Cladocerans sequester more phosphorus relative to nitrogen, potentially resulting in phosphorus deficiency for phytoplankton growth. We observed a positive relationship between meso-zooplankton communities with higher copepod relative to cladoceran biomass and levels of water column nitrogen deficiency. We also observed negative relationships between total precipitation over the 10 days prior to lake sampling and metrics of both nitrogen and phosphorus deficiency. These results support our predictions that relatively high watershed nutrient loading can overwhelm internal nutrient sources and sinks. However, when nutrient loading from the catchment is minimal meso-zooplankton community composition can affect nitrogen relative to phosphorus deficiency for primary production. Relationships between copepod biomass and nitrogen deficiency provide a potential mechanism for the high frequency of nitrogen limitation in Arctic Alaskan lakes.