Congruency using nonloricate ciliates as a surrogate to analyze taxonomic distinctness pattern of ciliated protozoan communities for assessing water quality was studied. The results showed that (1) with significant consistency with the total ciliate communities, the spatial pattern of nonloricate ciliates was significantly correlated with the changes of environmental status; (2) four taxonomic relatedness measures were significantly correlated with those of the total ciliate communities; (3) spatial variations in four taxonomic diversity indices of nonloricate ciliates were significantly related with the changes of environmental variables, especially nutrients; and (4) the paired taxonomic biodiversity indices of nonloricate ciliates showed a clear decreasing trend of departure from the expected taxonomic breadth in response to water quality. These results suggest that nonloricate ciliate assemblages can be used as a potential surrogate of ciliate communities to assess marine water quality using taxonomic distinctness measures, especially the paired indices based on presence or absence data.