Fomites involved in influenza transmission are either hand- or droplet-contaminated. We evaluated the interactions of fomite characteristics and human behaviors affecting these routes using an Environmental Infection Transmission System (EITS) model by comparing the basic reproduction numbers (R(0)) for different fomite mediated transmission pathways. Fomites classified as large versus small surface sizes (reflecting high versus low droplet contamination levels) and high versus low touching frequency have important differences. For example, 1) the highly touched large surface fomite (public tables) has the highest transmission potential and generally strongest control measure effects; 2) transmission from droplet-contaminated routes exceed those from hand-contaminated routes except for highly touched small surface fomites such as door knob handles; and 3) covering a cough using the upper arm or using tissues effectively removes virus from the system and thus decreases total fomite transmission. Because covering a cough by hands diverts pathogens from the droplet-fomite route to the hand-fomite route, this has the potential to increase total fomite transmission for highly touched small surface fomites. An improved understanding and more refined data related to fomite mediated transmission routes will help inform intervention strategies for influenza and other pathogens that are mediated through the environment.