Beds of the seagrass Zostera capricorni are an integral part of the estuarine landscape along the east coast of Australia, forming an important habitat for juvenile fish. Seagrass beds can vary in their size, shape and patchiness of seagrass cover as well as their distance from the estuary mouth. We tested for a correlation between these features and small fish assemblages in seagrass. Fifteen beds were selected from three size-categories (small, 980 to 2300 m2; medium, 3375 to 4090 m2; and large, 5335 to 6630 m2). We found that the size of beds, the patchiness of seagrass cover and location within the estuary (distance from estuary mouth) were all related to differences in fish assemblages. There were greater densities of fish species in small (10.3 ᰮ79 species .net-1) compared to medium (7.6 ᰮ6) and large (8.2 ᰮ5) beds. This occurred regardless of bed placement within the estuary, its patchiness or time of sampling (day and night). The fish assemblages within seagrass beds also changed as bed distance to estuary mouth increased. Six species had greater densities in beds closer to the estuary mouth, while only two species were in greater densities far from the mouth. Fish assemblages were different between beds with patchy and continuous cover, although total densities of all fish species combined were similar. There were greater densities of four species in continuous beds compared to two species that were greater in patchy beds. Overall, an important finding was that even small patchy seagrass beds contain greater densities of small fish species than larger beds with continuous seagrass cover.