Anxiety and depression in children and adolescents warrant special attention as a public health issue given their devastating and long-term effects on development and mental health. Multiple factors, ranging from genetic vulnerabilities to environmental stressors, influence the risk for the disorders. This study investigated the impact of environmental factors and genomics on anxiety and depression in children and adolescents across three cohorts: the Adolescent Brain and Cognitive Development Study (US), the Consortium on Vulnerability to Externalizing Disorders and Addictions (India), and IMAGEN (Europe). Linear mixed-effect models, recursive feature elimination regression, and LASSO regression models were used to identify the environmental impact on anxiety/depression. Genome-wide association analyses were then performed for all three cohorts with consideration of significant environmental effects. The most significant and consistent environmental factors were early life stress and school risk. A novel SNP, rs79878474 in chr11p15, was identified as the most promising SNP associated with anxiety and depression. Gene set analysis found significant enrichment in regions of chr11p15 and chr3q26, in the function of potassium channels and insulin secretion, particularly Kv3, Kir-6.2, SUR potassium channels encoded by the KCNC1, KCNJ11, and ABCCC8 genes, respectively, in chr11p15. Tissue enrichment analysis showed significant enrichment in the small intestine and a trend of enrichment in the cerebellum. The study highlights the consistent impact of early life stress and school risk on anxiety and depression during development and suggests the potential role of mutations in potassium channels and the cerebellum region. Further investigation is needed to better understand these findings.