The aim of this work is to determine the significant level of parameters such as sediment thickness, frequency and step size for data generated from electromagnetic (EM) simulator for sea bed logging (SBL) application that have been processed using cubic spline interpolation using Analysis of Variance (ANOVA) method. Synthetics data were generated from a simulator that is able to replicate SBL environment. SBL is a new technique that uses controlled source electromagnetic (CSEM) for finding resistive layers or hydrocarbon reservoir in deep water environment. It uses very low frequency to obtain greater wavelength for longer wave penetration. In this work frequencies of 0.5Hz, 0.25Hz, 0.125Hz and 0.0625Hz were used and sediment thicknesses were varied from 1000m to 3000m incremented every 250m. Collected data were interpolated using cubic spline with step sizes variation of 4,8,12 and 16 and mean square error (MSE) were calculated between original and interpolated data. The ANOVA method was applied to these MSE to study any significant different between frequency level and spline step size level at each sediment thickness. It was found from the ANOVA tables that frequency level and step sizes level were having significant difference to the MSE for every sediment thickness below 2250m. For sediment thicknesses of equal to 2250m and above, frequency level is not significance to the MSE but the step sizes level are still significant to the MSE. © 2012 IEEE.