In the context of the revision of the hydromorphological assessment framework for the environmental impact study (EIS) a method was developed to evaluate hydromorphological changes in natural, heavily modified and artificial waterbodies (BfG 2011). Based on the assessment framework, the module Valmorph (eVALuation of MORPHology) was developed in the context of the Integrated Floodplain Model INFORM (Rosenzweig et al. 2012, Quick et al. 2016). This module represents a quantitative approach to describe and evaluate the hydromorphological conditions of federal waterways. The testing, verification and optimization of the described method was done for exemplary investigation areas of the federal waterways. The Ems estuary was chosen to represent heavily modified transitional waters. In this context the indicator parameter suspended sediment budget was assessed by comparing reference to recent conditions. In this study, special focus is put on the challenges that are imposed by the specific characteristics of an estuary such as high temporal and spatial variability of suspended sediment concentration (SSC) and the changes in the system characteristics caused by anthropogenic impacts.