Wnt signaling plays crucial roles in embryonic patterning including the regulation of convergent extension during gastrulation, the establishment of the dorsal axis, and later, craniofacial morphogenesis. Further, Wnt signaling is a crucial regulator of craniofacial morphogenesis. The adapter proteins Dact1 and Dact2 modulate the Wnt signaling pathway through binding to Disheveled. However, the distinct relative functions of Dact1 and Dact2 during embryogenesis remain unclear. We found that and genes have dynamic spatiotemporal expression domains that are reciprocal to one another suggesting distinct functions during zebrafish embryogenesis. Both and contribute to axis extension, with compound mutants exhibiting a similar convergent extension defect and craniofacial phenotype to the mutant. Utilizing single-cell RNAseq and an established noncanonical Wnt pathway mutant with a shortened axis (), we identified specific roles during early development. Comparative whole transcriptome analysis between wildtype and and wildtype and compound mutants revealed a novel role for in regulating the mRNA expression of the classical calpain . Over-expression of phenocopies craniofacial dysmorphology. These results identify a previously unappreciated role of and calcium-dependent proteolysis during embryogenesis. Taken together, our findings highlight the distinct and overlapping roles of and in embryonic craniofacial development, providing new insights into the multifaceted regulation of Wnt signaling.