In recent years, salt marsh restoration projects have focused upon restoring hydrology through culvert enlargement to return functional values lost due to reduced tidal flow. To evaluate culvert effects on upstream nekton assemblages, fyke nets were set upstream of tidally restricted creeks, creeks recently restored with larger culverts, and paired reference creeks in New Hampshire and Maine, U.S.A. Subtidal habitats created or enlarged by scour were found immediately upstream of undersized culverts. All marshes supported similar assemblages and densities of fish, suggesting that marshes upstream of moderately restrictive culverts provide suitable habitat to support fish communities. However, densities of Crangon septemspinosa (sand shrimp) were significantly reduced upstream of culverts. A mark–recapture study was conducted in tidally restricted, restored, and reference marsh creeks to evaluate culvert effects on the movement of Fundulus heteroclitus (mummichog), the numerically dominant fish species in New England salt marshes. Recapture data indicated that small culvert size and consequently increased water velocity significantly decreased fish passage rates. We infer that upstream subtidal habitats and greater water velocities due to undersized culverts decreased nekton movements between upstream and downstream areas, resulting in segregated nekton populations. Restoration of salt marsh hydrology by the installation of adequately sized culverts will support increased fish access to marsh habitats and nekton‐mediated export of marsh‐derived production to coastal waters.