Land use and habitat quality have emerged as critical factors influencing the health, productivity, and survival of honey bee colonies. However, characterization of the mechanistic relationship between differential land-use conditions and ultimate outcomes for honey bee colonies has been elusive. We assessed the physiological health of individual worker honey bees in colonies stationed across a gradient of agricultural land use to ask whether indicators of nutritional physiology including glycogen, total sugar, lipids, and protein were associated with land-use conditions over the growing season and colony population size the subsequent spring during almond pollination. Across the observed land-use gradient, we found that September lipid levels related to growing-season land use, with honey bees from apiaries surrounded by more favorable land covers such as grassland, pasture, conservation land, and fallow fields having greater lipid reserves. Further, we observed a significant effect of total protein during September on population size of colonies during almond pollination the following February. We demonstrate and discuss the utility of quantifying nutritional biomarkers to infer land-use quality and predict colony population size.