Urban streams are under increasing threat from anthropogenic disturbances that alter their biological, chemical and physical characteristics. To attempt to repair the negative consequences of urbanization, management activities are commonly implemented with the aim of rehabilitating or restoring habitats. However, subsequent monitoring of these efforts is often done poorly or not at all. The setting of goals for these projects is also hindered by a lack of knowledge about the likely size of any potential response, and also the scope for undertaking activities at sufficient scales to override the likely larger-scale effects of urbanization. In this study, we completed a series of surveys in a large, urban estuary to generate information that can be used to assess the likely responses of fish to management activities aimed at rehabilitating estuary bank habitats. Initially, we mapped the banks of the estuary to describe the distribution of different potential habitat types for fishes. Surveys were then carried out to assess associations between fish and these habitats, with a view to providing an indication of the likely effect size that management works might produce. We then initiated a BACI (Before-After Control-Impact)-style monitoring design around management works aimed at stabilizing the banks of the estuary and increasing habitat complexity for fishes (the installation of coir logs and planting of native rushes). Power analyses based on the effect sizes and estimates of variability from our initial survey and subsequent monitoring respectively indicate that only large magnitude responses will be detectable. However, these are likely to be constrained by the influence of the larger-scale effects of urbanization. Even if localized responses occur, wider-scale manipulations to fish habitat in large urban estuaries are likely to be limited by a range of logistical, social and financial constraints that govern the scale and location of management activities.