Recent research has revealed that complex rice systems (CRSs), in which several plant and animal species, including azolla, fish, ducks and border plants have been integrated, can produce high and stable rice yields over time. However, the mechanisms that support these benefits have not been examined in detail. On-farm experiments were conducted in Indonesia during five rice cropping cycles. We compared three monoculture rice systems receiving chemical or organic inputs, and four organic polyculture rice systems that varied in level of complexity. To investigate the agro-ecological mechanisms of weed and pest suppression and nutrient cycling that determine rice productivity and stability, the dynamics of weeds, pests, nutrients and rice yields were monitored and related to rice system complexity. The observations revealed that increasing the level of complexity resulted in lower levels of weed and pest infestation. Analysis of duck behaviour and their gizzard composition showed that ducks foraged intensively on weeds, insects, and snails. Furthermore, nutrient cycling was accelerated by ducks via feeding and excretion as well as by their movement in the field. This could explain why rice yields increased along the gradient of complexity, and overall were higher and less variable in the most complex systems in comparison to the rice monocultures. In complex rice systems, increasing the number of species that are compatible to the rice ecosystems and could play a role in generating ecosystem services of weed and pest suppression as well as nutrient recycling, can lead to higher and less variable rice yields.