Drought exerts a strong influence on stream invertebrates by diminishing the area of surface water and altering habitat environment. However, the influence of drought-induced drying up on the longitudinal continuity of the distribution of stream invertebrate assemblages has remained largely unknown. We conducted a field survey to elucidate the influence of drought on the longitudinal continuity of the habitat environment and the community structure of stream invertebrates. Habitat environment and invertebrates were surveyed in the Shigenobu River in Japan every three months from May 2005 to November 2007 at fourteen study reaches, including three intermittent segments, established along the river. The longitudinal changes in the concentration of PO₄-P, periphyton biomass and the abundance of stream invertebrates in periods without drying up appeared to differ from those with. Changes in the community structure of stream invertebrates, in terms of the scores of non-metric multidimensional scaling, was more continuous during periods without drying up than those with. We concluded that drought modified the continuity of the longitudinal distribution of stream invertebrates by altering habitat environment at perennial river segments and by inhibiting downstream movement through intermittent river segments.