Maritime transport is crucial to the worldwide economy, with over 80% of global trade depending on sea routes and ports. The Mekong Delta is Vietnam’s leading producer and exporter of food, seafood, and fruit, contributing 31.37% to the agricultural Gross Domestic Product. However, waterway transport faces challenges, as over 70% of exports go through Ho Chi Minh City, raising costs by $10 to $15 per ton. To enhance port competitiveness, authorities must invest strategically in infrastructure and capacity while keeping costs reasonable. Developing a comprehensive evaluation model to assess seaport operators’ technical efficiency, technological capabilities, and productivity is essential. This study proposes a model that combines the Malmquist index and window data envelopment analysis to analyze the efficiency of inland ports in the Mekong Delta before and after the COVID-19 pandemic. The research consists of two stages: the Window DEA model tracks efficiency fluctuations among Decision-Making Units (DMUs); the Malmquist DEA model evaluates productivity changes over time. Results indicate that most DMUs maintained stability from 2019 to 2023, with technological innovations positively impacting performance. This study aims to provide insights into the port industry’s operations in Vietnam and guide the government and relevant agencies in making informed investment decisions to optimize budget allocation and enhance efficiency.