Viruses are the most abundant biological entities in marine and freshwater environments. Many studies have shown the ecological importance of viruses in the primary production and microbial food web in aquatic environments. However, no studies have examined viral abundance in the floodwater of paddy fields. The present study surveyed the abundance of virus-like particles (VLPs) and bacteria in the floodwater of a Japanese paddy field under a long-term fertilizer trial since 1925 during the rice cultivation period. Virus-like particles and bacterial abundances in the floodwater ranged from 5.6 × 106 to 1.2 × 109 VLPs mL−1 and from 9.2 × 105 to 4.3 × 108 cells mL−1 with mean abundances of 1.5 × 108 VLPs mL−1 and 5.1 × 107 cells mL−1, respectively, and increased with an increase in the turbidity of the floodwater with suspended particles. The magnitude of seasonal variation was more than 50-fold for VLP abundance and 100-fold for bacterial abundance. The virus-to-bacterium ratios fluctuated over the rice cultivation period, ranging from 0.11 to 72 and their increase correlated with the decrease in bacterial abundance. Our results suggest that viral abundance in the floodwater of paddy fields is larger than in natural marine and freshwater environments.