Native freshwater mussels form a critical component of benthic foodwebs, but are endangered worldwide, making their study an important conservation issue. Many unionids live in shallow environments where they are potentially vulnerable to natural disturbances, but the impact of physical forces on their growth and the role of sediments as a refuge is poorly understood. Here, we validate the use of two types of shell internal lines (nacreous, prismatic) as indicators of physical disturbance and shell coloration as an indicator of sedimentary habitat. We use these indicators to test (1) whether the sediments provide an effective refuge for juvenile and young adult mussels from natural disturbances and (2) whether disturbance events affect their growth. Elliptio complanata (Eastern Elliptio) emerge from the sediments when they are 20–50 mm in size and 2.5–7 years old. Juvenile and young adults lay down more disturbance lines at more exposed nearshore sites, but also in small lake basins with dense mussel populations. Disturbance lines are produced during both endo- and epibenthic growth periods, but in contrast to adults, they are not associated with growth anomalies. Sediments accumulating in shallow nearshore areas of lakes provide an imperfect but effective refuge for native mussels that warrant protection.