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Understanding habitat and water quality preferences of macroinvertebrates can provide important information to support biological assessments. The preferences of the nymphal stages of eight mayfly and five stonefly species were assessed from 650 stream sites in South Australia. The stoneflies showed similar preferences for flowing freshwater streams in cooler, wetter regions, with medium sized sediment ( particularly cobbles), dense riparian cover, low conductivity, low nutrients and high colour. The mayflies were more variable with two species preferring permanent, non-flowing pools throughout the State, including arid streams, while others occurred more frequently in streams where the annual average rainfall exceeds 600 mm. These preferences may provide additional information to help derive national water quality guidelines. Results from this study suggest that current trigger values for TN, TP, turbidity and possibly conductivity for south-central Australia may be too high to protect these insect orders. The assumption that all stoneflies and mayflies are sensitive taxa and indicative of high quality streams through the use of EPT metrics and family level identifications is questioned, particularly for semi-arid and arid streams where at least some baetid and caenid mayflies can tolerate harsh climatic conditions.