1. Rice feeds about half of the world's population. The intensification of rice farming has threatened biodiversity and ecosystem services, such as pest control. A growing body of evidence suggests that environmentally friendly rice farming (EFF) can be effective in biodiversity conservation. However, its dependence on spatial and temporal scales of EFF implementation and surrounding seminatural habitats has remained largely unknown.
2. We evaluated the effects of three types of EFF (organic farming, winter flooding and Integrated Pest Management [IPM]) against conventional farming on plants, spiders, and waterbirds in Japan. Through systematic surveys of 254 rice fields across rice production areas, we monitored EFF implementation at field and landscape scales, considering the time since transition to EFF and the surrounding seminatural areas.
3. EFF implementation at the field scale, such as organic farming, was found to have positive effects on plant richness and spider abundance, whereas the percent area of EFF fields within a 200-m radius positively affected Ardeidae abundance. However, as the percent area of surrounding semi-natural habitats increased, the difference in the plant richness between organic and other fields decreased.
4. Prolonged implementation periods of IPM or winter flooding, together with a reduction of more than 50% in synthetic fertilisers and pesticides from conventional agriculture, led to an increase in the spider abundance. Conversely, no clear positive effect of longer implementation periods of organic farming resulted in similar spider abundance in the three EFF types after 20 years.
5. Synthesis and applications. This suggests that the benefits of environmentally friendly rice farming depend on their spatial and temporal scales and the surrounding seminatural areas. We propose that such a context dependency should be considered in future policy. Our findings also provide a starting point for future research to test the mixed biodiversity benefits of EFF across cropland types and around the world.

These files contain processed data and R-code to examine the effects of environmentally-friendly rice farming and species richness or abundance of three taxonomic groups (plants, spiders and birds) in Japan, using generalised linear mixed models. The raw data were collected through field surveys and interviews with farmers. To protect the personal information of farmers, longitude and latitude are not provided in this dataset. The included R code generates statistics and working plots. Details on data processing and analysis can be found in the original publication and accompanying Electronic Supplementary Materials.

The R software is required to open the files provided.