A cost related study for the offloading operations is an integral part of monetary risks assessment. The partially standing waves which occur between the gap of vessels are responsible for impacting the offloading operations in terms of downtime costs. This paper presents a downtime cost analysis of side-by-side offloading operations in Malaysian waters for regular waves addressing the influence of partially standing waves through a graphical user interface (GUI). The developed interface is explained and its work procedure is demonstrated in this paper. The downtime is studied for two sea-states, beam and heading seas for which the probability of occurrence was calculated from the location specific wave scatter distribution. The results of wave kinematics for partially standing waves influencing the offloading operation for side-by-side configuration are presented. The down-time cost analysis will help the oil operator companies to analyze the economic risks involved for field developments and anticipate the loss in revenue for down-time occurrences. Overall, an attempt to integrate the influence of gap between vessels with offloading operations and related cost is presented. © 2020, Springer Science+Business Media, LLC, part of Springer Nature.