Continuum-scale models used to model and predict two-phase flow in the subsurface are often based on averaged flow parameters and do not consider pore-scale fluid flow phenomena, for example, ganglion dynamics and thin-film flow. As such, a major challenge in upscaling two-phase flow for groundwater engineering applications is understanding the impact of disconnected flow and ganglion dynamics on continuum-scale flow functions such as relative permeability-saturation and capillary pressure-saturation curves. In this study, we explored how changes in wettability and fluid velocity affect ganglion dynamics. We conducted pore-scale numerical simulations with OpenFOAM to investigate the displacement of decane by water. Additionally, we examined how displaced phase saturation (a continuum-scale flow function) responds to changes in dynamic fluid connectivity. We identified three different fluid flow regimes, that is, the connected pathway flow regime, ganglion dynamics (GD) flow regime, and droplet traffic flow regime, and studied the effects of changes in the wettability of the porous medium and the velocity of the invading fluid on the transitions between these different regimes. Our research showed that transitions between connected and disconnected pore-scale flow regimes, which are induced by changes in fluid velocity and wettability, have a significant impact on both fluid displacement efficiency and average fluid flow transport kinetics. The transport and confinement of hydrocarbons, organic pollutants or carbon dioxide (CO2) within rock pores is a complicated process that occurs on a minuscule scale and is crucial to groundwater engineering activities. The interplay of intricate fluid dynamics and alterations in rock and fluid characteristics at the microscopic level can have a considerable influence on continuum-scale flow properties. Continuum-scale models used to predict fluid flow in the subsurface are usually based on averaged flow parameters and do not account for the physics that occur at the pore scale. This often leads to disparities between the flow predictions made at the pore scale and at the field scale. A long-standing challenge in scaling up flow from the pore scale to the continuum scale lies in addressing the impact of disconnected fluid ganglia and ganglion dynamics on overall flow transport kinetics. This work aims to bridge this gap between the pore and continuum scales. We investigate the behavioral response of the saturation function (a continuum-scale function) to wettability and flow rate-induced changes in dynamic fluid connectivity. Changes in wettability and fluid flow rate induce transitions between connected and disconnected pore-scale flow regimes Transitions between pore-scale flow regimes have significant effects on the saturation function and flow transport kinetics The Lomeland, Ebeltoft, and Thomas (L-E-T) relative permeability model can capture the effects of pore-scale changes in fluid connectivity