Lake Naivasha was designated as a RAMSAR site in 1995. The lake environment is fragile and critically threatened by human-induced factors. The study presented a steady and transient numerical modeling. The long-term and system flux over time interaction between the lake and the surficial aquifer is represented in the Lake Package LAK3 with in the advanced 3-D simulation sofware (GMS). The model covers an area of 1817 km2. Model calibration was constrained by the observed groundwater and lake levels using PEST. The effect of excessive abstraction was rigorously analyzed via scenario analysis. The simulation was evaluated “with abstraction” and “without abstraction” scenarios. The abstraction scenario was simulated using range of combination assuming that all the abstraction was from the lake or the groundwater and in the ratio of groundwater and lake water. The effect of the stress was evaluated based on the observed aquifer heads and lake stage at the end of the simulation time. The development of low groundwater-level anomalies in the well field is explained. The result indicates that the one of the well fields is not in direct hydraulic connection to the main recharging water body. Apparently, similar development of cone of depression was not generated in the other two well fields, and this could have several reasons including due to the fact that these well fields are located relatively close by to the main recharging zones and concluded to have additional source of recharge, and this was supported by previous studies, whereby the isotopic composition of the boreholes has their source of recharge from precipitation and river and was also confirmed from the isotopic composition of unsaturated zone, which is a mixture of river and rain. The study reveals that seasonal variability of groundwater–surface water exchange fluxes and its spatially and temporally variable impact substantially on the water resource availability. Such analysis can be used as a basis to quantify the linkages between the surface water and groundwater regime and impacts in the basin. The model output is expected to serve as a basis via linking/coupling with others to incorporate the ecology and biodiversity of the lake to safeguard this high-value world heritage water feature.