Rice fields are temporary wetlands that harbor many of the same species that breed in natural temporary ponds. These systems have a complex limnology, characterized by rapid physical, chemical, and biological changes. The goal of this study was to evaluate the role of nutrients in the plankton and fish dynamics during a production cycle, based on the auto-ecology of the species related to their adaptations to environmental temporal changes in an irrigated rice field in Southern Brazil. The principal components analysis (PCA) indicated a temporal gradient driven by nutrient availability, grouping sampling periods according to the production cycle. ANOVA indicated temporal differences in the limnological variables during the development of the rice field production cycle. Linear regression showed a positive relationship between chlorophyll a, nutrients and biomass of small and medium filter-feeders. In contrast, planktivorous fish biomass was inversely related to chlorophyll a. This study showed both top down and bottom up processes simultaneously regulating the primary production in the rice field wetland along a temporal gradient the rice production cycle.