Nowadays, pesticides are used pervasively in Asian rice production areas. Nonetheless, information is scarce regarding chemicals’ application and synergistic toxicity and longer-term impacts on paddy ecosystems. In Phranakhon Si Ayutthaya and Ang Tong (AT) provinces, 40 conventionally and 31 organically managed farms were visited. The farmers provided information on types and levels of pesticides used, and indices describing pesticide ‘toxic exposures’ were calculated. In the dry and wet seasons, the fields were surveyed for soil organic carbon (OC) and nitrogen (N) and rice densities and sizes. Using multivariate statistics, interrelationships among variables were investigated. Overall, 12 types of herbicides (all synthetic), 27 insecticides (13 natural), and 6 molluscicides (1 natural) were recorded. Pesticide exposures differed between provinces; organic farms used more natural products. OC was positively correlated with ‘toxic exposure’ levels, probably resulting from effects of pesticides on carbon-reducing processes. Additionally, molluscicides and herbicides explained OC levels. N varied spatially, probably resulting from flooding regimes; management influences were unnoticeable. In the dry season, rice growth was decreased on fields exposed to plentiful synthetic insecticides, whereas in the wet season, use of herbicides and molluscicides enhanced the growth. Further research is advisable to better establish long-term costs and benefits of different pesticide regimes in rice fields.