Saltwater intrusion poses a serious threat to groundwater sustainability in coastal aquifers, particularly where both marine and estuarine tides interact with natural subsurface heterogeneity. Yet, the combined influence of marine and estuarine tides, together with subsurface heterogeneity, on saltwater intrusion in confined coastal aquifers is not well understood or adequately modeled. This study introduces a two-dimensional numerical model that applies a sharp interface approach and separates long- and short-term groundwater motions to simulate tidal effects on confined aquifers near estuaries. The model integrates stochastic log-hydraulic conductivity fields and captures both cross-shore and alongshore tidal boundary conditions. Analytical validation confirms high accuracy, with a relative absolute average error of 1.75 × 10−5 under steady-state conditions. Results show that increasing the standard deviation of hydraulic conductivity from δ = 0.0 to δ = 3.0 contracts the inland reach of tidal fluctuations from 2000 m to 350 m and reduces groundwater fluctuation amplitude at x = 200 m from 0.57 to 0.11 m. Tidal penetration distance drops by up to 60%. The interface toe migrates harmoniously, consistently lagging the tide by 0.25 periods, and its movement becomes irregular and guided by high-conductivity zones as heterogeneity rises. These spatial and temporal responses reveal that heterogeneity buffers inland freshwater but creates localized, high-risk zones for saltwater intrusion. The proposed model can directly support Sustainable Development Goal (SDG) 6 by guiding resource monitoring and SDG 13 by informing climate-resilient strategies. This approach is transferable to similar estuary-influenced aquifers worldwide, enabling sustainable water management.