Habitat fragmentation from natural or anthropogenic causes is a common phenomenon in shallow water marine habitats such as seagrass beds and oyster reefs throughout the world. Thus, habitat- and scale-dependent information on how organisms perceive and respond to changes in the landscape is critical to efforts aimed at predicting the effects of habitat change on population abundance. In estuarine systems, seagrass is considered one of the predominant nursery habitats for numerous ecologically and commercially important species; however, recent information suggests that alternative habitats such as oyster reefs may also be important sites for settlement and refuge. We used artificial seagrass- and shell-filled plastic trays placed on unstructured seafloor in Back Sound, North Carolina, USA to examine the interactive effects of Experiment, Patch size and Habitat type upon recruitment success of four species of decapod crustaceans: the grass shrimps, Palaemonetes intermedius Holthuis, P. pugio Holthuis and P. vulgaris (Say), and the blue crab, Callinectes sapidus Rathbun. Regardless of habitat type, all species of grass shrimp and J1 blue crab responded to habitat patchiness at scales as small as 0.25 to 4 m −2, whereas larger J2–J4 blue crab did not. Mean densities of all three species of grass shrimp responded in a similar manner to patch size, with significantly higher densities in the smallest patch size (0.25 m −2) compared to larger patches (0.5 to 4 m −2). Conversely, mean densities of J1 blue crabs were significantly higher in the largest patch size (4 m −2) compared to smaller patches (0.25 to 1 m −2). There was a negative and significant relationship between the density of grass shrimp predators and density of J1 prey, and no relationship between potential fish predators and J1–J4 prey. Thus, patterns observed for J1 may be dependent upon predators and not habitat patch size. Both species demonstrated different responses to habitat type depending upon relative densities and body size. Mean densities of P. intermedius and P. vulgaris were higher in seagrass than oyster shell during Experiment 1 (May) when shrimp were relatively abundant, but did not differ between habitat types during Experiment 2 (October), when densities were reduced 10-fold. Conversely, densities of P. pugio did not differ between seagrass and oyster shell. Mean densities of J1 blue crab were similar between seagrass and oyster shell, but higher in seagrass than oyster shell for later juvenile stages (J2–J4). Thus, blue crabs may rely equally on seagrass and oyster reefs as an initial settlement and refuge habitat for early juveniles. Our study demonstrates that an organism's response to habitat patchiness is species-specific, and that for a given species, the response is further modified by animal density and body size. The patterns observed in this study further highlight the importance of scale-dependent responses by mobile organisms to complex benthic habitats.