To understand hydrogen embrittlement and predict probable damage sites based on high hydrogen segregation, it is important to identify hydrogen distribution mechanisms in metallic microstructure with deformation. Hydrogen segregation in metals is affected by various factors such as grain-size, the character of grain boundaries (GBs), loading direction and strain-rate. To this end, a computational framework consisting of non-local dislocation density-based crystal plasticity model coupled with slip-rate based hydrogen transport model is presented to study the role of (i) grain-size, (ii) loading direction, (iii) strain-rate and (iv) GB character on hydrogen distribution and segregation in the pre-charged metallic microstructure. The computational framework is capable of accounting for the change in local hydrogen concentration due to prevailing hydrostatic pressure, trapping by dislocations, GB energetics and local slip-rates in the metallic microstructure. The difficulty in dislocation motion at the inter-granular regions of polycrystal due to high cross-hardening offered by geometrically necessary dislocations (GNDs) is incorporated in the model as additional isotropic hardening, whereas the back stress due to the GND pileups is included as a kinematic term in the flow rule. In addition, GNDs act as hydrogen trap sites leading to increased hydrogen concentration in the inter-granular regions. The strain-rate factor initially provided by Krom & Bakker (1999) is modified in the present work to make it compatible with the dislocation density-based coupled framework, which is able to calculate trapped hydrogen in dislocations along the slip systems. Plastically deformed polycrystals of various grain-sizes, along different directions, with varying strain rates and containing Σ3[11¯0](111) and Σ5[001](210) GBs show that the gradients of hydrostatic pressure and GB character are major factors controlling hydrogen segregation in the microstructure.