Oscillations in rainfall levels are one of the principal factors that determine seasonal shifts in physicochemical and hydrobiological variables, and exceptional climate events can have an enormous effect on the characteristics of small tropical estuaries. Given this, the present study investigated the responses of the physiochemical and hydrobiological variables of a small, shallow, and well-mixed Amazonian estuary with absence of any direct fluvial discharge to different climatic scenarios (typical conditions, and drier events). The study was based on 21 field campaigns conducted between April 2012 and April 2017. During rainy seasons of typical condition, when rainfall levels were higher and salinity lower than 7 (just after a weak La Niña), phytoplankton biomass was affected by increased turbidity (> 400 NTU) of the water, even when nitrogenous compounds were readily available (ammonium: 3.39 ± 1.71 µmol L−1, nitrite 0.90 ± 0.80 µmol L−1, and nitrate (3.91 ± 1.86 µmol L−1). In addition, the absence of any direct fluvial discharge appearance has contributed to the cumulation of phytoplankton biomass (chlorophyll-a > 20 mg m−3) into the estuary during the rainy season of the drier events and typical conditions, when turbidity was lower (< 200 NTU). Conversely, during the dry seasons of the drier events, when rainfall levels were lower, and extremes of salinity were recorded (> 38), phytoplankton biomass (chlorophyll-a < 10 mg m−3) was affected by the lower levels of nitrogenous compounds, even when phosphorous compounds were largely available. Overall, the present study has shown that extreme oscillations in rainfall levels cause abrupt shifts in the physicochemical parameters of the estuary, and affected the phytoplankton biomass, although high turbidity appeared to limit the buildup of this biomass. These effects are manifested immediately in the study area, given that the Taperaçu is a small estuary with a limited freshwater input, and it would seem reasonable to expect similar processes in other minor Amazonian estuaries when subjected to extreme fluctuations in rainfall levels.