Methods and systems for controlling processes related to the amount of fluid in a container subjected to externally-excited motions. Fluid level sensor measurements in processing tanks on-board boats are confused by ocean waves and swells. A hydrodynamic model of a fluid in a tank can be constructed using non-linear dynamic model algorithms with inputs such as multi-axis accelerations, fluid viscosity, and apparent level measurements. The model can be used to filter-out boat motion disturbances to obtain a corrected level of the fluid in the tank. The corrected fluid level signal can be further processed using a dynamic model of the tank and associated input and output flow rates in a closed loop observer. The methods and systems are especially advantageous for offshore equipment such as cementing and fracturing ships.