Autonomous underwater vehicles (AUV) are commonly used in many underwater applications. Recently, the usage of multi-rotor unmanned autonomous vehicles (UAV) for marine applications is receiving more attention in the literature. Usually, both platforms employ an inertial navigation system (INS), and aiding sensors for an accurate navigation solution. In AUV navigation, Doppler velocity log (DVL) is mainly used to aid the INS, while for UAVs, it is common to use global navigation satellite systems (GNSS) receivers. The fusion between the aiding sensor and the INS requires a definition of step size parameter in the estimation process. It is responsible for the solution frequency update and, eventually, its accuracy. The choice of the step size poses a tradeoff between computational load and navigation performance. Generally, the aiding sensors update frequency is considered much slower compared to the INS operating frequency (hundreds Hertz). Such high rate is unnecessary for most platforms, specifically for low dynamics AUVs. In this work, a supervised machine learning based adaptive tuning scheme to select the proper INS step size is proposed. To that end, a velocity error bound is defined, allowing the INS/DVL or the INS/GNSS to act in a sub-optimal working conditions, and yet minimize the computational load. Results from simulations and field experiment show the benefits of using the proposed approach. In addition, the proposed framework can be applied to any other fusion scenarios between any type of sensors or platforms.