This study describes the spatial and temporal dynamics of the copepod fauna in the estuary of the Caeté River, a highly dynamic environment characterized by a unique set of hydrological and hydrodynamic attributes. This ecosystem is part of the Amazon Coastal Zone (ACZ), which sustains one of the world's largest continuous tracts of mangrove forest. In the present study, a predominance of high‐energy conditions characterized by macrotides and strong tidal currents was observed throughout the year. Salinity (0.03 ± 0.05–40.00 ± 0.84) and temperatures (26.43 ± 0.10–30.08 ± 0.43 °C) were higher than during the rainy season at all sampling stations. The highest chl‐a concentration (3.92 ± 1.47–17.63 ± 2.60 mg·m−3) was recorded at the most oligohaline (innermost) station during the rainy season, while no spatial or seasonal pattern was found in dissolved nutrient concentrations, except for phosphates, which exhibited the highest concentrations during the dry season. A total of 22 copepod taxa was identified, of which the most abundant were Oithona hebes, Oithona oswaldocruzi, Acartia tonsa, Paracalanus quasimodo, Euterpina acutifrons and Pseudodiaptomus marshi. Copepodites and nauplii were also recorded. Mean total copepod abundance varied from 710.73 ± 897 individuals (ind.)·m−3 at the inner station to 236,486 ± 398,360 ind.·m−3 near the mouth of the estuary (outermost station). The results reflected rainfall‐influenced oscillations in hydrological variables, mainly salinity, which determined shifts in the distribution of copepods and their community structure within the study area. This pattern may be typical of estuaries in the ACZ with similar hydrodynamic and hydrological attributes that are not influenced by the Amazon River plume.