Ribonucleoprotein (RNP) germ granules are hallmarks of germ cells across the animal kingdom and are thought to be hubs for post-transcriptional regulation that promote formation of the germ cell precursors. While numerous RNAs are associated with germ granules in , the functions of many in germline development are poorly understood. Current methods for RNA knockdown, such as RNAi, do not allow local depletion of transcripts such as those found in the germ granules. We leveraged CRISPR-Cas13 to create a subcellular RNA knockdown system and tested it on two mRNAs, and , whose abundance in germ granules differs. Because Cas13 has both and cleavage activities, we evaluated the effect of target abundance on off-target RNA depletion. We show on and off-target RNA depletion is coupled when targeting the more abundant germ granule transcripts. Off-target RNA knockdown is less potent when the system is used for less abundant transcripts. When is knocked down in germ granules, we observed an increase in the calcium indicator GCaMP at the posterior and defective primordial germ cell migration, consistent with encoding a negative regulator of calcium signaling. In sum, we report an Cas13-based system for subcellular knockdown, evaluate its feasibility, and uncover a novel function for germ granule transcripts in promoting germline development.