Considering the demand for mooring larger ships at Brazilian port terminals, both private and public, in a scenario of growing exports, engineering interventions that can provide improvements in the vessel’s maximum allowed dimensions can represent significant profits. Hence, this work presents an approach of Nautical Bottom, defined as the minimum depth in which ships can navigate without significant adverse effects in ship control and maneuverability without physical damage, with the goal of raising the maximum ship draft allowed in nautical spaces with fluid mud beds. Due to its rheological properties, fluid mud, in general, allows for vessels navigate with low or negative under keel clearance, respecting the established Nautical Bottom concepts. In addition, fluid mud layer thickness at port areas can possibly vary according to hydrodynamics and sedimentologic variations. This article presents an analysis of fluid mud thickness variations within the Itajaí Port Complex (Santa Catarina, Brazil) turning basin, where fluid mud layers are up to 2.5 meters thick, by means of analyses of bathymetric surveys and numerical modeling. The Itajaí Port Complex is located at the Itajaí-açu river estuary, which presents high variability of river discharge and suspended sediments. From bathymetric surveys, it is possible to observe fluid mud thickness from 0.5 to 2.5 meters. Numerical simulation results indicate suspended sediment load as a main environmental aspect for fluid mud thickness variations in the study area.