The association of bed shear stress (tb) and porewater chemistry with the settlement and persistence of juvenile unionid mussels was examined in the Sydenham River (southern Ontario). The law of the wall was applied to vertical velocity profiles to estimate tb at 118 locations, in which porewater was sampled and sediments excavated. Twenty-six juvenile unionids (< 30 mm long) from five species were found in quadrats with 0.07 ≤ tb ≤ 0.77 Pa and large amounts of sand and fine gravels (> 2 mm). Logistic regression (tb and tb2) indicated that the highest probability of juvenile presence was where tb = 0.4 Pa. Principal Component Analysis indicated that in addition to tb, porewater dissolved oxygen, pH, specific conductivity and temperature were associated as habitat characteristic. These results provide new insights into the location of juvenile unionids in riverbeds, their habitat characteristics, as well guidelines for their conservation and reintroduction.