This study investigates the effects of different reference level (RL) criteria on dredging volume requirements for the Paraguay River, where recent declines in water levels, especially during dry seasons, pose challenges for safe navigation. Given that the Brazilian Navy’s traditional RL criteria rely on 20-year historical data, this may no longer reflect the river’s current hydrological conditions. To address this, were analyzed three RL scenarios: the standard 20-year RL, a critical-year RL from 2021 (an extreme drought year), and a recent 5-year RL based on the 94th percentile, which provides an adaptive approach to more recent conditions. Using a two-dimensional hydrodynamic model integrated with Geographic Information Systems (GIS), dredging volumes were calculated for each scenario. Results indicate that dredging requirements under the recent 5-year RL scenario are nearly three times higher than those estimated using the 20-year RL, reflecting the impact of declining water levels over the past decade. These findings suggest that adaptive RL criteria based on shorter, more recent time frames could improve river management, optimize dredging operations, reduce costs, and enhance navigational safety in response to increasing hydrological variability.