Proper breakdown of molecules within the lysosomal compartment is necessary to maintain the normal function of cells and their surrounding environment. The importance of this process in human health is stressed by a growing number of genetic diseases that involve defects in the proteins and enzymes responsible for this task. These diseases (termed lysosomal storage disorders or LSDs) have a diverse etiology, encompassing defects in individual acid hydrolases, metabolite transporters and enzymes that aid in targeting hydrolases to this organelle. Collectively, LSDs are one of the most frequently occurring genetic diseases affecting children in the U.S, with an estimated incidence of 1 in every 5000-7000 live births. Using zebrafish as a model system for developmental studies has many advantages which include but are not limited to large-scale experiment replication, early developmental genetic manipulation via the use of morpholinos, and microscopic phenotypical analysis in the early stages of embryogenesis. Surprisingly, there is little known regarding the early expression of lysosomal enzymes in zebrafish as well as overall yolk biology. To better gauge which lysosomal enzymes are best suited for morpholino based gene knockdown, developmental expression and regulation of zebrafish lysosomal enzymes were elucidated for enzymes that are well characterized in human disease. Several enzymes were then selectively targeted for morpholino-based knockdown, and the phenotypical and biochemical effects were analyzed. Additionally, the nature of several of these zebrafish lysosomal enzymes was better characterized by establishing pH activity profiles, yolk deposition, and percent mannose 6-phosphorylation, which yielded some novel findings in the zebrafish lysosomal biology.