With more than 80% of our energy needs being met by the subsurface environments, there is a significant interest in developing environmentally benign approaches to recover and store fluids in complex environments characterized by chemical and morphological heterogeneity and nanoscale porosity. However, the structure, dynamics, phase transitions, flow, and reactivity of confined fluids and colloids in nanopores differ from bulk fluids. These differences challenge the development of predictive controls on the organization, transport, and reactivity of confined fluids. To address this challenge, we harness computational molecular scale models in conjunction with experimental approaches including advanced synchrotron X-Ray and Neutron Scattering, and electron microscopy imaging to resolve the organization of compressed gases (e.g., CO2 and CH4), ice, and silica nanoparticles in pores with diameters smaller than 10 nm. The combined effects of the influence of solid interface and confinement on the organization of confined fluids and silica nanoparticles are elucidated. Approaches to quantifying the core-shell structure of confined compressed gases (e.g., CO2, CH4) in silica nanopores and phase transitions of confined ice are described. The influence of pore size and multi-component fluids on the diffusivity of confined CO2 is described. In the context of flow assurance in subsurface environments, the self-assembly of macromolecules such as asphaltenes in calcite and silica nanopores is discussed. One of the less studied but highly important considerations associated with the closing of pores in subsurface environments is due to silica scaling. The molecular-scale basis underlying the aggregation of silica nanoparticles at water-hydrocarbon interfaces and approaches to reverse this agglomeration using sodium dodecyl sulfate as a surfactant is described. The experimental methods, simulation approaches, and molecular scale insights of confined fluids can be applied translationally to advance low carbon energy and resource recovery and facilitate energy storage in subsurface environments.