This study was conducted as part of the first author’s Master’s research in Construction Management at Nepal Engineering College, with the corresponding author serving as supervisor. This study provides a comprehensive, evidence-based diagnosis of design documentation management practices in public lift irrigation projects in Nepal. Employing a sequential mixed-methods approach, the research integrates a systematic document review of 50 projects, surveys of 96 stakeholders, comprising 50 contractor representatives and 46 Department of Water Resources and Irrigation engineers, and key informant interviews. Analytical techniques include descriptive statistics, Kendall’s Tau correlation, mean response analysis, artificial neural networks (ANNs) for predictive modeling, relative importance index (RII), and thematic analysis using NVivo software. A significant “compliance paradox” was identified: while most stakeholders perceived the design documentation as adequate, no project achieved 100% compliance, with critical design artifacts such as operation and maintenance manuals and quality assurance plans consistently missing. External regulatory factors emerged as the most powerful determinant of design documentation quality (100% normalized importance from ANN), followed by human resource capacity (72%). Inadequate design documentation was directly linked to project delays (54.2% of respondents) and cost overruns (43.8%), while adequate documentation most significantly improved stakeholder coordination (RII = 0.817). The study proposes an actionable five-point blueprint for design process reform: standardized protocols, mandatory training, dedicated documentation officers, Electronic Document Management Systems, and enhanced stakeholder coordination. This paper is the first to provide a comprehensive mixed-methods investigation of design documentation management in Nepal’s public irrigation sector, contributing to design innovation for sustainable infrastructure development in resource-constrained settings.