This study investigates Enterprise Resource Planning (ERP) security vulnerabilities and their effects on data integrity, governance, and system performance in public-sector water utilities, with evidence from Gusii Water and Sanitation Company (GWASCO) and Kericho Water and Sanitation Company (KEWASCO). The study responds to the growing need for secure and reliable digital systems in public institutions, where data integrity is essential for transparency, accountability, and efficient service delivery. A convergent mixed-methods design was adopted, integrating quantitative data from 39 ERP users with qualitative evidence obtained through interviews, system-log analysis, observations, and document review. Descriptive and inferential statistics, including Chi-square and Fisher’s Exact tests, were applied alongside thematic analysis to assess vulnerabilities across key domains, including access control, audit trails, data integrity, insider threats, and system architecture. The findings indicate that average ERP data integrity was 60%, significantly below the expected benchmark of 90–100% for high-integrity enterprise systems. Major vulnerabilities included weak access-control enforcement, credential sharing, inconsistent implementation of role-based access control (RBAC), incomplete and editable audit logs, and persistent insider threats. Inconsistencies across ERP modules further demonstrate the influence of system architecture on data integrity. Inferential analysis revealed that most vulnerability domains operate independently (p > 0.05), while system architecture has a statistically significant influence on cross-module data consistency (χ² = 12.042, p = .001). The study concludes that ERP vulnerabilities are systemic and embedded within both technical and governance structures, with significant implications for transparency, accountability, and financial integrity in public-sector organisations. It recommends an integrated approach that combines strengthened access governance, secure audit-trail mechanisms, improved system architecture, and AI-enabled monitoring to enhance system integrity and support sustainable digital transformation.