A method for estimating properties of fluids in rock formations at selected locations within a geologic basin includes generating an initial model of the basin. The model includes as output spatial distribution of a rock formation mineral composition, rock formation porosity and composition of fluids in the rock formation porosity. An initial estimate of fluid composition is generated for a rock formation, and a sample of fluid is extracted from pore spaces of the rock formation. Composition of the fluid sample is analyzed from within, and the initial model of the basin is adjusted to substantially match the analyzed fluid composition. The adjusted model is used to generate an initial estimate of fluid composition.