Understanding surface water (SW)—groundwater (GW) interactions is essential for sustainable water management as these exchanges regulate streamflow, recharge, and ecosystem health. However, limited knowledge of their occurrence, distribution, and flow dynamics, exacerbated by climate variability and human activities, has contributed to water insecurity, emphasising the urgent need to investigate SW–GW interactions for reliable freshwater availability. This study addresses the lack of integrated modelling of SW–GW interactions by simulating their dynamics (1993–2022) in Kenya’s Amboni Basin using the coupled SWAT-MODFLOW. The results were calibrated following three steps: SWAT model with SUFI using one-gauge discharge, MODFLOW model with PEST using hydraulic conductivity, and final manual adjustments of key parameters for the coupled model. Using topography, soil, land cover, and meteorological data, the simulation showed strong SW–GW interaction, with average groundwater recharge of 3.3 m3/day and discharge of 220.2 m3/day to streamflow. The spatiotemporal GW recharge distribution from stream seepage and precipitation showed substantial variations, with most recharge occurring in April–May and October–November. Areas with higher elevations received more rainfall and higher recharge compared to low-lying regions. GW and SW interaction increased with increasing rainfall. However, it was noted that the recharge to GW has been decreasing since 2016, from a monthly average of 37.46 mm to 19.58 mm, despite variations in rainfall. Effective water resource management in the Amboni Basin requires stricter regulation of groundwater and surface water extraction and conservation efforts to protect water towers and sustain recharge processes.
Understanding surface water (SW)—groundwater (GW) interactions is essential for sustainable water management as these exchanges regulate streamflow, recharge, and ecosystem health. However, limited knowledge of their occurrence, distribution, and flow dynamics, exacerbated by climate variability and human activities, has contributed to water insecurity, emphasising the urgent need to investigate SW–GW interactions for reliable freshwater availability. This study addresses the lack of integrated modelling of SW–GW interactions by simulating their dynamics (1993–2022) in Kenya’s Amboni Basin using the coupled SWAT-MODFLOW. The results were calibrated following three steps: SWAT model with SUFI using one-gauge discharge, MODFLOW model with PEST using hydraulic conductivity, and final manual adjustments of key parameters for the coupled model. Using topography, soil, land cover, and meteorological data, the simulation showed strong SW–GW interaction, with average groundwater recharge of 3.3 m3/day and discharge of 220.2 m3/day to streamflow. The spatiotemporal GW recharge distribution from stream seepage and precipitation showed substantial variations, with most recharge occurring in April–May and October–November. Areas with higher elevations received more rainfall and higher recharge compared to low-lying regions. GW and SW interaction increased with increasing rainfall. However, it was noted that the recharge to GW has been decreasing since 2016, from a monthly average of 37.46 mm to 19.58 mm, despite variations in rainfall. Effective water resource management in the Amboni Basin requires stricter regulation of groundwater and surface water extraction and conservation efforts to protect water towers and sustain recharge processes.