In this paper, a monitoring and modelling concept for ecological optimized harbour dredging and fine sediment disposal in large rivers is presented. According to the concept, first a preliminary assessment should be performed previous to the dredging and dumping procedure to derive knowledge about the current status in hydrodynamics, morphology and instream habitat quality. During the performance of the maintenance work, a high-resolution monitoring program has to be organized to measure flow velocities, the suspended sediment concentrations and the extent of the occurring plume. These data can then be compared with natural suspended sediment conditions and serve as input data for numerical sediment transport modelling. Furthermore, bathymetric surveys and biotic sampling enable the detection of possible effects of dredging and disposal in the post-dumping stage. Based on sediment transport modelling approaches, short- to mid-term developments of the sediment plume can be predicted with an additional and final habitat evaluation at the end of the project. This concept was applied and optimized during the maintenance work at the case study winter harbour Linz at the Danube River. The findings of the presented study highlight the necessity of integrated monitoring and modelling approaches for harbour dredging especially in large river systems.