Desalination and water reuse are important means to resolve local water scarcity and security issues worldwide where membrane distillation (MD) may be part of a solution. Natural organic matter and in particular, humic acids (HA), are widely present in water supplies to be treated but exhibit little understood behavior to diffuse through MD membranes into permeate. In this work, air gap (AGMD) and water gap (WGMD) were utilized to study HA behavior in MD using seawater and synthetic water over a range of typical MD temperatures, flow rates and membrane types. HA diffusion was first shown with seawater feed then on synthetic solutions at all process conditions. While electrical conductivity rejection was always above than 99%, HA rejection showed values of 33% and 90% for AGMD and 68% and 93% for WGMD with seawater and synthetic water, respectively. Analytical techniques were used to perform a preliminary organic matter characterization in permeate, obtaining clear differences between the feed and permeate HA property. Compared to hydrophobic membranes, uniquely oleophobic membranes inhibit HA diffusion suggesting hydrophobic surface diffusion of HA through the membrane. HA flux as well as potential undesirable effects of the organic matter in permeate should be considered for MD applications.