Flooded rice fields can provide habitats for wetland species and ecosystem services similar to those of natural wetlands. During the last three decades, however, farming practices and management systems have been intensified in many rice-producing countries. In addition, more recent socioeconomic changes have caused agricultural abandonment in some parts of East and Southeast Asian countries such as Japan. This study reviewed long-term statistics on rice farming, as well as the impact of agricultural intensification and abandonment on farmland biodiversity at multiple spatial scales in Japan. The impact of pesticide use was greatest in the 1950s–1970s, when the use of highly toxic agents had not yet been prohibited. More recently, different components of agricultural intensification have been the largest threat for various taxa, for example, chemical pesticides for aquatic plants and invertebrates and modern efficient irrigation/drainage systems for amphibians, fishes, and waterbirds. The negative impacts of agricultural abandonment on farmland species have been rapidly increasing with the expansion of abandoned fields and the subsequent vegetation succession and loss of habitat heterogeneity. We also discuss the effectiveness of environmentally friendly farming practices, including the reduced use of pesticides, winter paddy flooding, and installation of fishways, to reduce the negative impacts of agricultural intensification on farmland species in rice-paddy landscapes.