The temporal and spatial patterns of summer extreme low flows and effects on stream ecosystems were evaluated throughout the Otago Region of the South Island of New Zealand during a severe drought in 1998–1999. Flows, water quality, and aquatic biology were monitored bimonthly at 12 locations as part of a long-term regional monitoring programme and results were evaluated and compared among summer 1998–1999 and all previous summers, as well as among three major subregions. Flows during the drought were extremely low for prolonged periods in many locations, particularly in North Otago. At most sites temperatures were slightly higher for a longer period than during other summers. In predominantly agricultural/pastoral catchments, widespread bacterial contamination of streams occurred due to increased livestock use of watercourses and decreased dilution during low flows. Concentrations of other contaminants derived from non-point sources, including nitrogen, phosphorus, and sediment, decreased in many locations due to the lack of rainfall and runoff events. Electrical conductivity generally increased as a result of the lack of dilution and increased evaporation and groundwater inputs. Overall water quality was worst in agricultural catchments in South Otago, and returned to conditions prior to the low flows by late autumn in most areas.The diversity of benthic macroinvertebrate communities and number of sensitive taxa decreased somewhat in many locations, but the magnitude and duration of these effects were not great. Differences between summer 1998–1999 and other periods, and among subregions, were not significant. Although some differences in low flows and effects on stream ecosystems across a range of landscapes and catchments can occur, the rapid recovery of water quality and benthic macroinvertebrates in most locations indicates that many streams are resilient to extreme low flows and drought with minor long-term effects.