Mathematical model of sediment has become an essential research approach to predict erosion and deposition in estuaries. However, the further development of the model was limited by the related physical parameters. According to this limitation, it analyzed some key problems involved in the mathematical model for estuarine sediment transport. From the perspective of vertical integration of the three dimensional differential equation, the result of the equation analysis shows that the recovery saturation coefficient should be greater than 1 unit theoretically; it indicated that the sediment non-uniform coefficient, relative particle size and sediment consolidation all have some effects on erosion/deposition process of estuary, provide suitable mathematical expressions for cohesive force of arbitrary K gradation, incipient probability and critical incipient shear stress of non-uniform cohesive sediment in estuary, discussed the role of critical deposition shear stress in dealing with the flocculation of fine sediment. It argued that it will be more reasonable that the formula for sediment transport capacity of flow is determined by the water and sediment parameters corresponding to the maximum or minimum sediment concentration than by the averaged ones in theory. And also, it presented the formula for carrying capacity of unsteady water; pointed out the numerical calculation and the problem of imperfect verification.