Marine reserves are an important management tool for conserving local biodiversity and protecting fragile ecosystems such as seagrass that provide significant ecological functions and services to people and the marine environment. With humans placing ever-growing pressure on seagrass habitats, marine reserves also provide an important reference from which changes to seagrass and their ecological assemblages may be assessed. After eight years of protection of seagrass beds (Posidonia australis) in no-take marine reserves (Sanctuary Zones) within the Jervis Bay Marine Park (New South Wales, Australia; zoned in 2002), we aimed to assess what changes may have occurred and assess continuing change through time in fish assemblages within these seagrass meadows. Using baited remote underwater videos (BRUVs), we sampled seagrass fish assemblages at three locations in no-take zones and five locations in fished zones three times from 2010 to 2013. Overall, we observed a total of 2615 individuals from 40 fish species drawn from 24 families. We detected no differences in total fish abundance, diversity, or assemblage composition between management zones, although we observed a significant increase in Haletta semifasciata, a locally targeted fish species, in no-take marine reserves compared with fished areas. Fish assemblages in seagrass varied greatly amongst times and locations. Several species varied in relative abundance greatly over months and years, whilst others had consistently greater relative abundances at specific locations. We discuss the potential utility of marine reserves covering seagrass habitats and the value of baseline data from which future changes to seagrass fish populations may be measured.