Cranberry agriculture is a major land use in parts of the New Jersey Pinelands, USA. We compared the composition of genus-level macroinvertebrate assemblages collected from three habitats (muck, vegetated muck, and woody debris) in 12 New Jersey Pinelands blackwater streams draining forest, abandoned-cranberry bogs, and active-cranberry bogs and evaluated whether variations in macroinvertebrate assemblages were related to differences in land uses within the associated drainage basins. All 12 streams were relatively slow moving and acidic, with low conductance values and dissolved-oxygen concentrations. Muck was the dominant substrate at most stream sites. Many of the taxa that we encountered are adapted to lentic habitats, slow-moving lotic habitats, or low-oxygen environments. Macroinvertebrate composition differed significantly between the active-cranberry streams and the other two stream types and was associated with a complex environmental gradient represented by variations in dissolved oxygen, temperature, specific conductance, stream width, and woody debris. Overall, the effect of stream type appeared to overshadow that of the three different habitats. Although we cannot conclude that subtle between-site differences in dissolved oxygen were responsible for variations in community composition, many of the genera associated with the forest and abandoned-bog/active-cranberry ends of the community gradient are reported to have contrasting tolerances to low-oxygen levels. The relationship between reduced canopy cover and both lower woody-debris cover and higher stream temperatures, which can influence dissolved-oxygen levels, was most likely related to forest-canopy removal associated with historic- and active-cranberry agriculture.