We assessed two dimensions of stream connectivity: longitudinal (between forest patches along the stream) and lateral (riparian vegetation), using macroinvertebrate assemblages as bioindicators. Sites representing different land-uses were sampled in a lowland basin that holds a mosaic of protected areas. Land-use analysis, forest successional stages and riparian zone widths were calculated by the GIS analysis. Macroinvertebrate fauna was strongly affected by land-use. We observed a continuous decrease in the number of sensitive species, %Shredders and IBE-IOC biotic index from the upstream protected area to highly deforested sites, increasing again where the stream crosses a Biological Reserve. When analysing buffer strips, we found aquatic fauna responding to land-use alterations beyond the 30 m riparian corridor (60 m and 100 m wide). We discussed the longitudinal connectivity between forest patches and the riparian vegetation buffer strips necessary to hold high macroinvertebrate diversity. We recommend actions for the increase/maintenance of biodiversity in this and other lowland basins.