Water-filled treeholes are important habitat patches for aquatic invertebrates in forest ecosystems. A detailed understanding of the interspecies relationships that occur within them will help in understanding how invertebrate diversity is maintained in forests, particularly with respect to resource utilization. The sequential use of the same food resource among several different species is called a processing chain. In this study, we focused on the aspects of leaf litter in the treeholes as a food and habitat resource, and tested the following hypotheses using artificial containers as treeholes with three different leaf litter samples categorized as “untreated”, “fragmented”, and “pulverized”: (1) inorganic ions would leach out as leaf fragmentation progresses, resulting in water acidification, which consequently affects invertebrates. (2) filter-feeder species that consume microorganisms and fine particle organic matter increase as leaf fragmentation progresses. (3) differences in the size of leaf litter fragments affect the inhabitant species and cause differences in the assemblage structure of invertebrates. We observed an increase in pH and dissolved oxygen (DO) with increasing the fragmentation of leaf litter; however, the results were marginally non-significant. The assemblage composition of aquatic invertebrates did not show clear patterns in relation to the leaf litter treatments. Invertebrate assemblages from treeholes with pulverized leaf litter appeared to be associated with increasing DO. We found that the filter-feeder Tripteroides bambusa (Diptera: Culicidae) was dominant under conditions where treeholes contained fine particles of leaf litter, while the benthic inhabitant Ceratopogonidae sp. (Diptera) dominated under conditions with coarse leaf litter fragments. Our results suggest that fragmentation of leaf litter may have different effects on the different dominant species. We conclude that resource processing does not necessarily have positive effects on the species.