Sediment has profound effects on water quality. Correspondingly, water quality modeling often needs sediment transport modeling. However, simplified descriptive sediment transport was originally employed for water quality modeling, and the linkage between sediment transport models and water quality models is less developed. Therefore, the main purposes of this study were to develop general methods of coupling sediment transport and water quality models and to improve sediment transport modeling for water quality modeling. Linkage of sediment transport and water quality was discussed and a comprehensive sediment transport literature review was conducted. SEDDEER (Sediment Deposition and Erosion), a stand-alone sediment and contaminant fate and transport model, which simulates one water box and the underlying multiple sediment bed layers, was developed. SEDDEER for Visual Basic for Application (SEDDEER_VBA) was written in VBA. SEDDEER for FORTRAN (SEDDEER_FOR) is the corresponding FORTRAN model. To improve WASP in terms of sediment transport, SEDDEER_FOR was incorporated into the WASP TOXI7 module as the starting point to generate the coupled WASP model (WASP_SEDDEER). Verification and validation of SEDDEER_VBA were conducted prior to model application and incorporation. A comprehensive model test was performed to show that SEDDEER_FOR is computationally identical to SEDDEER_VBA. Simple tests were carried out to verify the fluxes across the sediment-water interface and ensure that the coupling of the WASP water column and SEDDEER bed models is correct. The testing results indicated that these models were verified and/or validated. SEDDEER was used to evaluate the effects of sediment on contaminant transport. WASP_SEDDEER, WASP7.4, and EFDC were applied to Mobile Bay to demonstrate the capabilities of WASP_SEDDEER, and WASP_SEDDEER produced a reasonable and consistent modeling result. The results of the study indicated that SEDDEER can be used for one-box sediment and contaminant fate and transport modeling, and also incorporated into water quality models. In addition, WASP_SEDDEER coupling was implemented correctly and can be applied to the real world. Finally, study results show that sediment affects contaminant fate and transport mostly by external forcing and flow conditions, and contaminant fate and transport varies with different sediment and contaminant characteristics and sediment transport processes.