We investigated ten environment factors of habitat conditions of Lefua echigonia (Endangered Species) in small irrigation streams of Yato during an irrigation period and a non-irrigation period in 2002. Study area was three Yatos in Zushi-onoji Historical Environmental Conservation Area, Tokyo. Then the relationship between the existence of this species and the environmental factors at each period was analyzed. As the result, it was indicated that during the irrigation term, affective factors to the habitat of this species were physical environmental factors, substrate type and the presence of paddy fields on sides of stream. During the non-irrigation term, chemical environmental factors, substrate type and water velocity affected the habitat. Therefore, it was suggested that conservation measures should be different at each period.