Macroinvertebrate communities in lotic networks are structured by local environmental (biotic and abiotic), dispersal and stochastic processes. Rare species comprise a large component of community richness and their populations can be threatened by environmental change more than common species’ populations. However, they are often excluded from analyses as “noisy” data, thus not contributing the information they carry and not being accounted for in catchment management decisions. We studied the effect of stream network position and dispersal mode on common and rare benthic macroinvertebrate assemblages, in three catchments in the central North Island of Aotearoa New Zealand. Rare taxa assemblages did not differ between headwaters and mainstem streams and were not structured by either the local environment or dispersal processes. Their inclusion, however, did not mask patterns in common species assemblages and in some cases even amplified them. The small study area and its dense stream network allowed weak dispersers to closely track suitable environmental conditions, while strong dispersers had much higher dispersal potential, masking their relationship to the environment. Contrary to expectations, mainstem streams were not more species rich and diverse than headwaters. Flooding events are common in New Zealand streams and might have an overriding effect on mainstem communities. Headwater communities comprised a uniform group because of the streams’ habitat similarities and dense lotic network within the small, protected area, contrasting the fewer and affected by differing land-use types, mainstem communities. Community structure was clearly differentiated between the two network positions and driven more by the local environment than dispersal processes. Inclusion of rare species did not hinder analyses in a metacommunity context but provided greater certainty instead. Conservation planning for rare stream macroinvertebrate biodiversity requires consideration of the whole catchment, including both headwaters and mainstem reaches.