To exploit its socio-economic functions, engineering measures are regularly applied in estuaries. Estuaries are, however, known to be very complex systems. Stemming from this complexity is the generation of a so-called estuarine turbidity maximum (ETM), which poses great siltation problems to the engineering measures. An engineering measure, which is looked upon in this thesis, is a trench accommodating for the construction of a submerged tunnel. Despite the complexity of estuaries, trench siltation rates are predicted in practice by simple empirical engineering tools. However, a lot of uncertainty is associated with the predicted trench siltation rates, as such engineering tools do not capture the complex estuarine mechanisms. These mechanisms are found to dominate the sediment supply to the trench and the subsequent trapping of sediment in the trench. Therefore, in this thesis, it is investigated to which degree of certainty trench siltation rates in estuaries can be predicted, based on a process-oriented and engineering-oriented viewpoint. This is researched according to the implementation of a detailed process-based numerical model, which is considered to be highly accurate. For this purpose, the following case study is adopted: a trench near the ETM of the well-mixed Scheldt Estuary, at Oosterweel, Belgium. The uncertainty of the numerical model is estimated based on a sensitivity analysis, which maps the epistemic uncertainty, and a scenario analysis, which approximates the intrinsic uncertainty. For verification purposes, modelling results are compared with the state-of-the-art theory on trench siltation mechanisms, and estuarine sediment transport and trapping mechanisms. These are thoroughly analyzed in this thesis based on an extensive literature study. Additionally, a link to practice is made by comparison of the degree of certainty and practicality of the numerical model with the engineering tools. It could be estimated, based on the parameter uncertainty, that the epistemic uncertainty of the numerical model equals approximately 1.5 times the expected siltation volumes. A similar uncertainty due to intrinsic uncertainty was estimated, as the trench siltation rates showed a strong dependency on the variation in forcing regarding tide, river and storms at sea. In total, this led to a quantifiable uncertainty in the order of 2.5 times the expected siltation volumes. Regardless of this uncertainty, great confidence is put in the performance of the numerical model, as in accordance with existing literature of the study area and theory on well-mixed estuary, important mechanisms in the supply of sediment to the trench were found to be: salinity-induced circulation, tidal rectification, Stokes’ drift and river discharge. Additionally, the governing sediment trapping mechanisms of the trench, found by the model, are in line with state-of-the-art literature. In contrast, yet unidentified by literature, the longitudinal salinity gradient over the estuary also seem to dominantly influence the trapping efficiency of the trench, in particular during flood in which it induces a strong decrease in sediment trapping. In comparison, it is believed that engineering tools, applied for trenches in estuaries, are prone to very high epistemic uncertainty caused by model inadequacy. This is because stand-alone application of the engineering tool on the problem gave a significant over-estimation of the siltation volumes, as predicted by the numerical model. Furthermore, the engineering tool was found to behave differently within a tidal cycle, and on changing environmental conditions. Above epistemic uncertainties due to model inadequacy could, however, not be quantifiably supported, as the total quantifiable uncertainty was in the same order of the numerical model. In conclusion, the degree of certainty of the trench siltation rates is believed to be improved significantly using a detailed numerical model instead of engineering tools. However, a huge drawback of the application of detailed numerical models, is the complexity and the impracticality of the numerical model. Therefore, this thesis opts for the development/use of a more sophisticated semi-empirical tool for engineering measures in estuaries. Though, more research is recommended on trenches in both similar and different type of estuaries in order to generalize and confirm the findings of this thesis.