Many endangered species are freshwater organisms, particularly those inhabiting rivers, and conserving their habitats is therefore critical. River habitat complexity has been recognized as an important factor for biodiversity both in Japan and globally. Outside Japan, habitat restoration using coarse woody debris (CWD) has been widely implemented; however, functional differences among CWD with different morphologies remain poorly understood. Structurally complex CWD, such as branched wood, not only reflects the presence of diverse riparian tree species including broadleaved forests but also indicates the continuous supply of woody debris to river ecosystems. To clarify how morphological differences in CWD influence river ecosystems, we compared physical environments and leaf litter retention around CWD with-branches (hereafter, with-branches sections) and CWD without-branches (hereafter, without-branches sections) in the headwaters of the Kushiro River, eastern Hokkaido, Japan, and examined whether differences occurred in aquatic biota. Benthic invertebrate assemblages differed between with-branches and without-branches sections during the flood season. Several predator taxa were observed in with-branches sections, whereas grazer taxa dominated without-branches sections. Assemblage composition in with-branches sections was influenced by the accumulation of particulate organic matter (POM), while that in without-branches sections was associated with gravel aggregation. In with-branches sections, both bottom-up and top-down effects influenced biodiversity index. The accumulation of POM in with-branches sections originated from litter directly trapped by CWD, and litter-associated invertebrate assemblages were also diverse. The presence of both types of woody debris in the creek enhances benthic invertebrate diversity, highlighting the importance of habitats that locally concentrate substrates, particularly gravel and POM, and suggesting that introducing, retaining, or ensuring the continuous input of diverse woody debris is crucial for the conservation of aquatic and riparian biota.