Branchiopods, ostracods, and copepods were surveyed in ricefields of Shiga Pref., Japan. For a taxonomic inventory of microscopic organisms, sampling took place at 11 diverse sites (4-7 paddies each) in 2009. Temporal changes in micro-crustacean assemblages in experimental paddies with and without introduced larval crucian carp (Carassius auratus grandoculis) were monitored by repeated sampling during the planting season in 2007 and 2009 and examination of fish gut contents. The effect of soil moisture on large branchiopod occurrence was checked on the basis of winter soil cores taken in areas where 5 of Shiga’s 7 species occur. In the fish larva study, Bosmina longirostris was pumped in initially with irrigation water but never dominated. Moina spp. (mainly M. macrocopa) were soon dominant, but then disappeared from paddies with fish while also declining elsewhere. About 20 days post-flooding, other cladocerans were abundant, but only Scapholeberis kingi persisted in paddies with fish. As for ostracods, Ilyocypris spp. were abundant from about 10 days, and Hemicypris ovata and Cyprinotus uenoi from 20 days post-flooding, but all then declined with fish present. Copepods (8 spp. out of 14 recorded from all surveyed paddies) were little affected by fish. Occurrence and abundance of the clam shrimp Caenestheriella gifuensis were significantly dependent on low winter moisture at soil depths of 5-10 cm.