Past hurricanes in the United States have highlighted the structural vulnerability of bridges exposed to storm surge and wave loads, triggering the development of fragility models. These models are essential for estimating the likelihood of structural failures in bridges during extreme events to support risk mitigation and resilience enhancement. However, the literature still lacks fragility models that can accommodate the effects of spatial variability of surge and wave loads and bridge characteristics like superstructure type and span slope. In addition, the presence of different types of superstructure within the same bridge necessitates the development of fragility models which can handle such variations. In this light, first, this study develops fragility models for individual spans of different bridge classes (concrete girder, steel girder, slab, box girder) considering spatial variability of wave loads and variations in structural characteristics. Herein, nonlinear dynamic analyses are employed for calculating the structural response and stepwise logistic regression is used for deriving the predictive fragility models. Then, a bridge system fragility assessment framework is proposed for system reliability assessment of the entire bridge, which accounts for different types of superstructures within the bridge and partially correlated span failures. In order to demonstrate the application of the fragility models and the system fragility assessment framework for regional level risk mitigation, the performance of bridges in the Houston-Galveston region is evaluated for two storm scenarios. The results show that the system failure probability obtained using no correlated span failure assumption is close to the actual failure probability obtained using the proposed approach highlighting the effects of correlations (or the lack of) on the system fragility.