In the ecological drainage ditches and wetlands downstream of various integrated rice–frog agroecosystems, aquatic plants were arranged to block, absorb, deposit, or transform nitrogen, phosphorus, and other chemical substances in paddy runoff. Integrated rice–frog agroecosystems can address the problem of excessive applications of paddy fertilizers and chemical pesticides, as well as the consequences of serious nutrient loss and pollution. In integrated rice–frog agroecosystems, a paddy field is considered to be an agricultural ecosystem that can be regulated and the rice is an ecological factor in that agricultural ecosystem. Integrated rice–frog agroecosystems in paddy fields can be designed to combine chemical fertilizer and pesticide source control technologies, internal process blocking, and output interception technology for pollutants using various planting and breeding strategies. The experiment showed that microbial agents play a significant role in promoting rice growth. To reduce the seed bank of weeds in the paddy, soil preparation and field irrigation were done as usual before rice planting.