To evaluate the salinity stress on ecological quality using protozoa, a 1-month baseline study was conducted along a gradient of salinity 9, 19, 29, 39, and 49 PSU (practical salinity unit). Samples were collected from an intertidal zone of the Yellow Sea, northern China. The findings demonstrated that (1) protozoan species represented different tolerance to scales of salinity stress; (2) the species richness decreased with increase of salinity, while in individual abundances sharply dropped with both increase and decrease of salinity compared to the control (29 PSU); (3) the probit regression revealed the median inhibition concentrations (IC₅₀) values were 21.14 and 38.24 PSU for low (<29 PSU) and high (>29 PSU) situations, respectively; and (4) high salinity stress significantly shifted the community pattern of the protozoan fauna. Therefore, it is suggested that periphytic protozoan communities may be used a useful bioindicator of ecological quality under salinity stress in marine ecosystems.