Diurnal groundwater level fluctuations (DGLF), closely tied to the metabolic rhythm of wetland vegetation, offer insights into direct groundwater consumption. This study is centered on exploring the spatial and temporal patterns of DGLF within the riparian aquifer of the Upper Biebrza region, motivated by the need to understand those sub-daily ecohydrological dynamics at play in this ecosystem, on a process-oriented scale. Through integrated spatiotemporal multivariate analysis, we aim to identify the key potential factors driving variations in these fluctuations across the landscape gradient, as well as, at different time scales. The study employed a comprehensive approach to gather data on groundwater heads and direct groundwater fluxes, utilizing high-temporal-resolution wells within a monitoring network. Meteorological variables from a dedicated station and high-resolution remote sensing maps were also integrated into the dataset. Analysis revealed distinct seasonal patterns and correlations in diurnal groundwater fluctuations, closely correlated with air temperature, solar radiation and subsequently vegetation phenology. Soil moisture content and summer rainfall events also influenced the intensity of these diurnal fluctuations. Dry periods intensified fluctuations, indicating an elevated reliance on groundwater by phreatophytes, while fluctuations decreased after rainfall events, signaling a shift in vegetation’s water source preference to soil moisture. Based on integrated data interpretation, a couple of potential mechanisms, reasonably forming the spatial variation pattern of DGLF, were formulated. Notably, the influence of local hydraulic gradients at transitional forest landscape edges, where higher amplitude fluctuations occurred, compared to lower fluctuations at midpoints. The proximity to the peat-mineral interface influences diurnal fluctuations, with wells closer to the interface showing sustained high-amplitude fluctuations driven by higher rates of recharge. Additionally, the influence of river proximity was explored, revealing dampened fluctuations in wells closer to the river due to rapidly changing hydraulic gradients. Further systematic experimentation, including numerical and data-driven modeling, is needed to validate these hypotheses. The study findings provide perspectives into (DGLF) patterns and distributions, enabling more accurate groundwater evapotranspiration (ETg) estimation and opening new avenues for considering ecohydrological feedback regarding carbon–water interaction, in relation to the daily-scale water table position.