In floodplains, rotifers are among the most abundant zooplankton organisms and play an important role in ecosystem functioning. Here, we evaluated the distribution of six feeding guilds of rotifers including filter C1 (body size: <200 µm), filter C2 (body size: >200 to <600 µm), filter C3 (body size: >600 to <1000 µm), filter C4 (body size: >1000 µm), suctor, and predator for 11 years. We also analyzed the relationship between guild distribution and environmental parameters (i.e., chlorophyll‐a, phosphate, nitrate, ammonia, and inorganic suspended matter). Finally, we investigated the relationship between feeding guilds heterogeneity (abundance inconsistency) and environmental heterogeneity. Sampling occurred every 3 months from 2000 to 2010 in six shallow lakes of the Upper Paraná River floodplains. Filters C1, Filter C2, and suctors were the dominant feeding guilds. Nitrate and chlorophyll‐a shaped the temporal distribution of the guilds. An intermediate value of environmental heterogeneity was correlated with greater feeding guilds heterogeneity, potentially indicating that intermediate disturbance in the environmental variables may allow for greater differences in abundance distribution between rotifer guilds in shallow floodplain lakes. Our study elucidated the role of rotifers in food resource consumption, energy transfer, and competitive relationships in response to temporal environmental heterogeneity in subtropical floodplains.