A hydrostratigraphic model has been proposed based on the spatial distribution of aquitards, aquifers, aquicludes, recharge discharge areas, salinity, mineralization, hydraulic head, diagenesis, and biodegradation information overlain with source rock potential, nature, and dispersal of hydrocarbons in the Mandapeta-Endamuru area, Krishna Godavari rift basin. This has resulted in understanding the verticolateral hydrodynamics and accumulation of gaseous hydrocarbons and variance in their geochemical properties. Three hydrogeologic systems are identified within the Mesozoic, and the associated gaseous hydrocarbons are characterized by their wetness and fingerprint Gastar diagrams. Temporal distribution of the salinity isolith in the vertical geologic column defines the intensity of meteoric infiltration and saline water percolation. In the Mandapeta subbasin, older formations are found to be less saline than the younger ones, indicating salinity inversion. Reservoirs of higher hydraulic heads are associated with gaseous hydrocarbons. The observed variation in hydraulic heads of the Mandapeta and Gollapalli aquifers is attributed possibly to the intervening Red bed aquitard acting as a seal. Areas of fault conduits are identified that facilitated the upward migration of hydrocarbons while allowing the percolation of infiltrated waters and further causing selective segregation of minerals. Vertical superimposition of different hydrogeologic systems and relative formation contacts also controlled the diffusion and nature of gaseous hydrocarbons. A composite hydrogeologic model has been framed based on studies for understanding the recharge discharge dynamics incorporating seismic inputs.