Groundwater systems affected by various factors can exhibit complex fractal behaviors, whose reliable characterization however is not straightforward. This study explores the fractal scaling behavior of the groundwater systems affected by plant water use and river stage fluctuations in the riparian zone, using multifractal detrended fluctuation analysis (MFDFA). The multifractal spectrum based on the local Hurst exponent is used to quantify the complexity of fractal nature. Results show that the water level variations at the riparian zone of the Colorado River, USA, exhibit multifractal characteristics mainly caused by the memory of time series of the water level fluctuations. The groundwater level at the monitoring well close to the river characterizes the season-dependent scaling behavior, including persistence from December to February and anti-persistence from March to November. For the site with high-density plants (Tamarisk ramosissima, which requires direct access to groundwater as its source of water), the groundwater level fluctuation becomes persistent in spring and summer, since the plants have the most significant and sustained influence on the groundwater in these seasons, which can result in stronger memory of the water level fluctuation. Results also show that the high-density plants weaken the complexity of the multifractal property of the groundwater system. In addition, the groundwater level variations at the site close to the river exhibit the most complex multifractality due to the influence of the river stage fluctuation.