Managing the impacts of anthropogenically enhanced deposited fine sediment levels in lotic ecosystems requires understanding of how catchment land-use changes have altered the natural sediment regime (erosion, transport, deposition) of rivers. Unfortunately, no existing studies have employed an appropriate sampling frequency over a period encompassing the full range of seasonal flow conditions expected to influence in-stream sediment dynamics. We determined the short-term (monthly) dynamics of deposited fine sediment and invertebrate communities over 12-months in 15 fourth- and fifth-order rivers draining catchments of low, medium and high land-use intensity in Southland, New Zealand to determine when and where fine sediment threatens stream health. We compared the Quorer resuspension method (suspendable inorganic sediment, SIS) and the in-stream visual sediment cover assessment method, and evaluated the effectiveness of four commonly-used invertebrate stream health metrics against their newly developed sediment-specific counterparts. Monthly variability in SIS was substantial across all land-use categories, but became more pronounced as land-use intensity increased. All 15 sites experienced a prolonged period of relatively stable flow which coincided with the largest short-term increase in SIS at 14 of the 15 sites. However, variability in SIS was not mirrored in macroinvertebrate metrics. These findings suggest that controlling inputs of fine sediment to rivers and streams will be most effective when targeted at periods of prolonged stable flow, particularly within high land-use intensity catchments. The resuspension method consistently outperformed visual estimates when considering its relationship with macroinvertebrate metrics, while sediment-specific metrics demonstrated a stronger association with fine sediment than commonly employed metrics e.g. (%EPT). We conclude that restoration/mitigation practices cannot be based solely on short-term, or even long-term, reductions in fine sediment, or on physical measures alone, but should be based on long-term recoveries of sediment-impacted invertebrate communities using concurrent measurements of both biotic and abiotic conditions.