During severe drought and low flows in the Otago Region of the South Island of New Zealand, increased bacterial contamination of rivers occurred in agricultural/pastoral catchments due to greater stock use of waterways and the lack of dilution and flushing flows. Concentrations and loadings of nitrogen and phosphorus generally decreased due to the lack of rainfall, runoff and transport from diffuse sources. Other analytes, including dissolved solids and pH, did not change to any considerable degree and were quite spatially variable. Although the health of benthic macroinvertebrate communities can decrease with a lower diversity and fewer sensitive taxa, effects were not significant in most rivers. Algal blooms occurred in some locations, particularly in lowland agricultural catchments with low water velocities and little shade. The prolonged lack of flushing flows can be a significant problem. Fish kills occurred where they became stranded and isolated from the main flow and where there was a lack of deeper pool refuges. Temperatures in excess of 25°C can also result in isolated fish kills, but the duration of these high temperatures appears to be the most critical factor. Adverse effects from drought can be widespread and severe in some locations, but appear to be relatively short-lived with recovery occurring rapidly with increasing flows at most locations. This indicates a degree of resilience of rivers to drought and low flows with long-term impacts that are not severe