Small amounts of water can enter diesel fuel during usage, causing major damage and failure of engine parts. Water is dispersed in fuel as droplets stabilized by the presence of surface-active compounds in the original fuel mixture as well as in fuel additives, including lubricity improvers and deposit control agents. Additives partition to the fuel-water interface and lower the interfacial tension (IFT), decreasing the ability to coalesce and separate water from fuel. The ability of standard coalescing filters to capture and coalesce emulsion droplets depends on dynamic IFT, conventionally measured for large millimeter-sized drops or planar interfaces. In this work, a microfluidic platform is employed to generate a monodisperse stream of small micrometer-sized water droplets in model fuel and ultralow sulfur diesel, mimicking the size of droplets in actual fuel-water emulsions. The deformation of hundreds of droplets is tracked at high speed through twenty-six geometric contractions to find time-dependent apparent IFT. It is found that the time scale associated with the decrease of IFT is orders of magnitude smaller in micrometer-sized droplets compared to millimeter-sized drops from pendant drop experiments. This finding suggests that, in real emulsion processing conditions such as fuel filtration, the residence time of droplets from the point of formation to filtration is such that IFT has already decreased to the equilibrium value. This work results in clear implications that standardized tests used by industry for qualifying diesel fuels must be reconsidered to account for droplet size, to enable design of efficient fuel filtration systems.