The southern sector of the Llanos Basin in Colombia is a heavy and extra-heavy crude oil province where it has been hypothesized that hydrodynamic flow has influenced the potential of hydrocarbon storage and production. In this area, the hydrodynamic flow and the geochemical nature of the fluids are thought to decrease the potential for hydrocarbon retention. This work provides a comprehensive view on the impact of the regional hydrodynamic flow on the retention of the heavy oil accumulations present in the reservoirs that are part of the most important regional flow unit identified in the Southern Llanos Basin. The Basal Flow Unit (BFU) constitutes a basin-scale flow unit that hydraulically and laterally connects rocks from the Cretaceous (west) to the Oligocene (east) and extends from the basin's southwestern margin up to hundreds of kilometers within the Llanos foreland basin, and whose main water recharge zone has been identified towards the eastern flank of the Serranía de la Macarena. To understand the impact of the physicochemical properties of the fluids on hydrocarbon retention, we analyze the relationship between hydraulic data and the main characteristics of the fluids present in the BFU as well as their spatial distribution. This analysis integrated information from hydraulic heads, SARA analysis (Saturates, Aromatics, Resins, and Asphaltenes), Whole Oil Gas Chromatography analysis, API-gravity, and oil densities. In addition, hydrochemical analyses of the primary ions were performed in groundwater samples from the BFU, which was integrated with deep resistivity data measured in producing and exploratory oil wells in the area. The results allowed identifying the southwestern corner of the southern Llanos Basin as the area with the highest hydrodynamic flow impact, and therefore, the area with the least potential for hydrocarbon retention. We attribute the main causes to: 1) the proximity to recharge areas, and 2) the low contrast of fluids densities (freshwaters and highly biodegraded heavy crude oils), implying high Tilt Amplification Factor (TAF) values (10–100). In addition, the highest values of hydraulic heads (200–400 m), groundwater with the lowest ion concentrations (up to < 5 ppm Cl−), highly biodegraded crude oils, and the presence of poorly developed geological structures with low dip angles occur in this area, which allows us to interpret that the water washing process has decreased the hydrocarbon retention potential for this sector of the Llanos basin. Furthermore, gradual changes in resistivities (decreasing eastward) and ions concentration (increasing eastward) in groundwaters suggest the eastern flank of the Serranía de la Macarena as the main recharge zone of meteoric waters into the BFU. Finally, numerical simulation techniques were used to analyze the behavior of hydrocarbon drainage under hydrodynamic conditions, obtaining a first approximation to the average linear groundwater flow velocities between 10−3 and 10−4 ft/day.