Iron is an essential trace element for living organisms, and it plays an important role in redox reactions in aquatic environments. Although many studies have investigated the application of iron materials to improve water and sediment quality, their negative effects remain unknown. Therefore, this study investigated the effects of three iron materials, i.e., zero-valent iron, iron oxide, and iron oxyhydroxide, on common benthic organisms in a coastal area via exposure experiments. In the exposure experiments, Paraprionospio patiens, a marine polychaete, exhibited abnormal behavior immediately after the addition of zero-valent iron, and the average survival rate after 14 d decreased significantly (Scheffé's test: p < 0.05). This is the first study to show that zero-valent iron on the sediment surface negatively affects the survival of P. patiens. Although Iron materials are often used to improve aquatic environments, their potential adverse effects should be addressed through continuous monitoring after use.