Estuaries are dynamic ecosystems with crucial environmental, economic, and social functions, driving extensive hydro-morphological research supported by numerical modeling. This study systematically reviews estuarine modeling applications over the past 15 years to identify commonly used tools, model configurations, and validation strategies, to examine regional trends in the application, and to explore and discuss the relative emphasis on hydrodynamic, sediment transport, and morphological modeling within the selected studies. Following the PRISMA 2020 methodology, a comprehensive search in Scopus and Web of Science identified 3926 articles, from which 197 met the eligibility criteria. Each study was analyzed to assess modeling software, mesh types, dimensional configurations, and validation parameters. Results indicate that DELFT3D is the most widely used tool, followed by TELEMAC and FVCOM, with a preference for two-dimensional models and structured meshes. Model accuracy, assessed through Skill Scores, confirms their reliability in representing estuarine dynamics. Additionally, findings reveal significant geographical disparities, with China leading research efforts, while Latin America and Africa remain underrepresented. This gap highlights the need to expand modeling efforts in these regions to enhance estuarine management and resilience. Strengthening numerical modeling in diverse contexts will improve the predictive capacity of hydro-morphological processes, supporting sustainable decision-making in estuarine environments.