Piezoelectric and triboelectric nanogenerators are unique devices that convert mechanical energy, e.g., fluid motion or mechanical vibration into electrical energy. Their significant advantages, such as their small scale, eco-friendly operation, and adaptability to various conditions, including humid, vibrating, and temperature-variable environments, make them perfect for green energy harvesting in aquatic and windy contexts. However, the interaction between the fluid and the specific design of the related energy-harvesting machine is complex. Advanced computational fluid dynamics (CFD) methods enable the simulation of complicated interactions of fluids and structures, leading to a better understanding of the effects of fluid flow on energy conversion efficiency. This review article discusses the role of CFD in design optimization and performance improvement of piezoelectric and triboelectric nanogenerators for renewable energy harvesting applications in harsh environments. Selecting an appropriate and effective CFD method coupled with other numerical methods that can accurately simulate the complex multiphysics, including fluid motion interaction, material stress, and electromechanical coupling, in piezoelectric and triboelectric nanogenerators will enable optimum design at reduced manufacturing and experimental testing costs. This paper provides an applicable guideline for using CFD tools to model energy harvesting devices that utilize piezoelectric and triboelectric nanogenerators and enhance their efficiency.