Estuarine assemblages are exposed to multiple disturbances that overlap in time and space. Along the Atlantic Intracoastal Waterway (east coast, United States), two disturbances that frequently co-occur are the production of wake by boats and the disposal of sediment dredged from boat channels. Boat wake generally coarsens sediments by eroding finer particles while deposition of dredge spoil decreases mean gram size. If previously demonstrated effects of boat wake on infauna are due to coarsening of grain size, deposition of dredge spoil on wake affected sites may, through compensatory effects, prevent an effect of wake from being detected. Epifaunal assemblages associated with seagrass blades that are more likely to be structured by hydrodynamic forces than granulometry may instead be affected by boat wake irrespective of the previous deposition of fine materials. To test these hypotheses, infauna and epifauna were sampled in patchy seagrass habitat at sites with and without boat wake that were affected by historic deposition of dredge spoil and at sites without wake that had not received dredge spoil. Sediment granulometry and infaunal assemblages differed between sites with and without dredge spoil but not between spoil affected sites differing in exposure to wake. Epifaunal assemblages differed between sites with and without wake irrespective of sediment granulometry. The effect of wake on epifauna was primarily due to lesser abundances of the gastropod Bittiolum varium and the slipper limpet, Crepidula fornicata, at wake exposed sites. These results suggest that because of their opposing effects on sediment granulometry, boat-wake and sediment disposal may have compensatory effects on infaunal assemblages. The detection of an effect of wake on epifauna despite the absence of a sedimentological effect of the disturbance shows that ecological impacts do not necessarily mirror physical effects and should be considered separately when adopting strategies of management.