Bottom fishing is an important source of anthropogenic disturbance affecting seafloor habitats across the world’s continental shelves. Minimizing these disturbances is a key objective of ocean management; however, opportunities to meet this objective have been hampered by limited information on the spatiotemporal extent and dynamics of fishing impacts. To improve our ability to assess and understand impacts to seafloor habitats, we: 1) developed a flexible and cohesive framework (i.e., the ‘Fishing Effects’ model) to assess impacts over large spatial and temporal domains, 2) implemented the Fishing Effects model on regional and global scales, and 3) leveraged the Fishing Effects model within a statistical framework to better understand the disturbance dynamics of biogenic organisms. First, we developed the Fishing Effects model to estimate the areal extent of habitat disturbance that incorporates information on fishing activity, fishing gear characteristics, and vulnerabilities of seafloor habitat features. We implemented the model in the North Pacific, estimating that habitat in 3.1% of the 1.2 million km2 study area was disturbed through 2017. A 24% decline in habitat disturbance was evident since 2010 attributable to a single regulatory gear change which lifted trawl gear components off the seafloor. We then implemented this model globally, estimating that 2.9% (1.08 million km2) of the world’s continental shelves are currently impacted by fishing – a level of impact we found comparable to land use for terrestrial-sourced protein. Finally, we developed a statistical framework that integrates the Fishing Effects model with species distribution models. The integrated modeling framework allows for estimation of the post-impact recovery times of biogenic organisms and their susceptibility to fishing disturbance. We applied the integrated model to deep water corals, sponges, and sea whips in the Eastern Bering Sea and estimated the mean recovery time to be 9 years, 7 years, and 1 year, respectively. Corals and sea whips were found to be twice as susceptible to removal from fishing disturbance compared to sponges. Ultimately, the tools developed here provide flexible frameworks to better address critical gaps in our understanding and assessment of seafloor habitats and promote sustainable management of wild caught fish.