The aim of the present study is to estimate the different chemical fractionations of copper (Cu) and selenium (Se) in coal samples of different coal mining areas. The Cu and Se bound to various chemical fractions of coal collected from two mining fields of Sindh, Pakistan, have been determined by BCR sequential extraction scheme (BCR-SES). The long duration of the BCR sequential scheme (51h) was reduced by a time-saving shaking device (ultrasonic bath) termed as ultrasonic-assisted extraction (USE) depending on the same operating conditions and extracting solutions used for BCR sequential extraction scheme. The both trace elements were determined in aquifer water, sampled from different depth of both coal mining fields. In addition, the groundwater of dug well in the vicinity of coal mining areas were also analyzed for Cu and Se using reported extraction methodologies. The partitioning of Cu and Se bound with different chemical fractions of coal was successfully made by proposed USE, within 2h as compared to long duration of BCR-SES (51h). The Cu and Se concentrations in acid-soluble fractions of coal samples were > 10%, enhanced by USE extraction procedure than those values gained via BCR-SES (p < 0.01). About 67 to 69% of Cu were found in the first three fractions, whereas their remaining amount corresponding to 31 to 33%, respectively bound with crystalline/residual fraction, while up to 66.1 to 71.1% of total Se contents extracted in three extractable phases, followed up to 28.9 to 33.8% of it was bound with residual phase. The concentrations of Cu and Se in groundwater of different aquifers were found in decreasing order as AQ1 > AQII > AQIII; the same trend was observed for two aquifers of Lakhra coal mining, whereas the groundwater samples have two to three folds higher levels of Se than WHO limit. The Cu levels in water samples were significantly lower than the recommended limit of WHO for drinking water (p < 0.01).