Environmental and macroinvertebrate data collected across a range of spatial and temporal scales are synthesised to investigate factors influencing invertebrate community structure and composition in soft-bottomed streams ( 50% of streambed substrata in sand-silt) of northern New Zealand. A total of 75 macroinvertebrate taxa was recorded from sand-silt substrata at 13 Waikato sites (54 taxa) and 8 Northland sites (53 taxa) where faunas were dominated by Ephemeroptera, Trichoptera, Chironomidae, and Mollusca. Differences in upstream geology, climate, land cover, and hydrology, potentially coupled with biogeographic factors, appeared to contribute to a regional separation in invertebrate community structure (taxa presence-absence). In the Waikato, site-specific conditions had a stronger influence on community structure and composition than substratum (sand-silt, macrophyte or wood). However, within sites, substratum type had strong effects on macroinvertebrate communities that persisted through time. On macrophytes, faunal composition varied considerably over time and among sampling patches, reflecting phenological shifts in the species and biomass of plants present, successional changes in invertebrate taxa, and micro-scale variations in water velocity. Macrophytes can provide important sites for energy transfer, although pathways leading to invertebrate nutrition appeared site-specific and temporally variable. Collectively, these data point to a spatio-temporal hierarchy of factors that influence invertebrate community structure and composition in soft-bottomed streams. The major differences compared with stony streams occur at the micro-to meso-scales, with greater significance of nonbenthic substrata (wood and macrophytes) as invertebrate habitat and sites of energy transfer in soft-bottomed streams, and the temporally variable influence of changing macrophyte biomass on local hydraulic conditions and water quality. To help reduce the effects of high spatial and temporal variability and obtain a representative picture of reach-scale conditions for stream health assessment purposes, long-term invertebrate monitoring of softbottomed streams should incorporate all velocity and substrata conditions, and aim to collect samples at a consistent stage of the macrophyte phenological cycle.