High rate sound speed profiling systems have the potential to maximize the efficiency of multibeam echosounder systems (MBES) by increasing the accuracy at the outer edges of the swath where refraction effects are at their worst. In some cases, high rate sampling on the order of tens of casts per hour is required to capture the spatio-temporal oceanographic variability and this increased sampling rate can challenge the data acquisition workflow if refraction corrections are to be applied in real-time. Common bottlenecks result from sound speed profile (SSP) preprocessing requirements, e.g. file format conversion, cast extension, reduction of the number of points in the cast, filtering, etc. Without the ability to quickly pre-process SSP data, the MBES operator can quickly become overwhelmed with SSP related tasks, potentially to the detriment of their other duties. A series of algorithms are proposed in which SSPs are automatically pre-processed to meet input criteria of MBES acquisition systems, specifically the problems of cast extrapolation and thinning are addressed. The algorithmic performance will be assessed in terms of sounding uncertainty through a series of case studies in a variety of oceanographic conditions and water depths. Results from a field trial in the French Mediterranean will be used to assess the improvement in real-time MBES acquisition workflow and survey accuracy and will also highlight where further improvements can be made in the pre-processing pipeline.