The present study focused on the synthesis and application of novel isocyanate-modified carrageenan polymers as sorbent materials for pre-concentration and removal of diclofenac (DCF) and carbamazepine (CBZ) in different aqueous matrices (surface waters and wastewaters). The polymer materials were characterized using Fourier transform infrared spectroscopy (FTIR), X-ray diffraction (XRD), Thermal Gravimetric Analysis (TGA) and Scanning Electron Microscopy (SEM). The effects on the adsorption behavior were studied, and the equilibrium data were fitted by the Langmuir and Freundlich models. The maximum adsorption capacity (Q_max) was determined by Langmuir–Freundlich model and was ranged for iota-carrageenan (iCAR) from 7.44 to 8.51 mg/g for CBZ and 23.41 to 35.78 mg/g for DCF and for kappa-carrageenan (kCAR) from 7.07 to 13.78 mg/g for CBZ and 22.66 to 49.29 mg/g for DCF. In the next step, dispersive solid phase extraction (D-SPE) methodology followed by liquid desorption and liquid chromatography mass spectrometry (LC/MS) has been developed and validated. The factors, which affect the performance of D-SPE, were investigated. Then, the optimization of extraction time, sorbent mass and eluent’s volume was carried out using a central composite design (CCD) and response surface methodology (RSM). Under the optimized conditions, good linear relationships have been achieved with the correlation coefficient (R²) varying from 0.9901 to 0.995. The limits of detections (LODs) and limits of quantifications (LOQs) ranged 0.042–0.090 μg/L and 0.137–0.298 μg/L, respectively. The results of the recoveries were 70–108% for both analytes, while the precisions were 2.8–17.5% were obtained, which indicated that the method was suitable for the analysis of both compounds in aqueous matrices.