Large-scale genomic studies have uncovered numerous genes linked to schizophrenia and autism. However, the specific impact of these genes on brain development and function remains unclear. Using optimized pipelines for high-throughput whole-brain activity mapping and behavioral profiling, we have established larval zebrafish phenotypes of mutants for genes linked to autism, childhood-onset schizophrenia, and typical schizophrenia. Human mutations modeled in zebrafish include protein truncation, amino acid substitution, or copy number variation. Using brain activity mapping, we uncovered convergent phenotypes for genes involved in autism, as well as commonly affected brain areas. For several lines, we used RNA sequencing to define molecular drivers of the observed phenotypes, identifying targetable disruptions in neuropeptide signaling, neuronal maturation, and cell proliferation. Beyond the larval screen, we discovered abnormal social interaction at 21 dpf for three mutants for autism-linked genes and identified possibly involved pathways using RNA-sequencing. Ultimately, we expect in-depth studies of these zebrafish lines to nominate downstream targets of disease genes for rational drug development.