Human activities have resulted in significant release of rare earth elements (REEs) into the environment. However, the pathways of REEs from waters and soils into freshwater food webs remain poorly understood. Recent studies suggest that aquatic invertebrates may be good biomonitors for REEs, yet there is little information on factors that control REE bioaccumulation in these organisms. Our goal was to study the environmental drivers of REE levels in zooplankton, a key component in plankton food webs, across lakes from geographic areas with different bedrock geology. From 2011 to 2014, bulk zooplankton samples were collected for REE analysis from 39 lakes in eastern Canada. We observed a more than 200 fold variation in surface water REE concentrations and a 10-fold variation in sediment REE concentrations. These concentration gradients were associated with a range of more than an order of magnitude in zooplankton REE concentrations (∑REEY 3.2-210 nmol g-1). We found higher REE bioaccumulation in zooplankton from lakes with lower pH and higher REE to dissolved organic carbon ratios. Bioaccumulation was also strongly linked to the free ion concentrations of REEs (REE3+) in surface waters. Our study suggests that zooplankton REE bioaccumulation is an excellent predictor of bioavailable REEs in freshwaters.