Tributary junctions are points in river networks where there can be an influx of organic matter and inorganic sediment. Addition of materials at tributary junctions is likely to alter food availability and habitat for aquatic organisms. We surveyed junctions of upland cobble-bed streams (stream orders 1–4, 2.2–10.8 m wide) in the Acheron River catchment (or watershed) in Victoria, Australia, to determine whether tributaries were an important source of suspended particulate matter, and whether benthic organic matter and coarse wood density increased at tributary junctions. We conducted measurements in high (austral spring 2005) and low flows (austral summer 2006) seasons. There were no systematic patterns in concentrations of suspended particulate matter with respect to positions within confluences (tributaries, upstream mainstem, downstream mainstem and confluence). However, total exports of suspended particulate matter in high-flow appeared to be the summation of exports from the upstream mainstem and the tributary in an approximate ratio of 2:1. In low flow, the 2:1 ratio was similar but the downstream mainstem value was similar to the upstream mainstem value (i.e., no clear summation). The fraction of organic matter in the suspended particulate matter did not depend on position within the junction, but was about 19% higher in the low-flow season. Tributaries had lower amounts of benthic organic matter than any measured positions in the mainstem, which themselves were indistinguishable. However, benthic organic matter was positively related to discharge ratio (tributary:mainstem), which may indicate that smaller, upriver junctions, which tended to have higher discharge ratios, were associated with higher standing crops of benthic organic matter. The distribution of coarse wood (logs and branches C10 cm diameter) was asystematic with respect to position in the junction. Overall, tributaries had little effect in these junctions, with the most evident effect being an increase of about one-third in exports of suspended particulate matter when flows are high.