Anthropogenic land use can alter water chemistry, habitat availability, and macroinvertebrate assemblages in nearby aquatic ecosystems. Low-gradient streams are especially understudied and vulnerable to these changes. This study aims to address how water chemistry and habitat availability affect macroinvertebrate assemblages in low-gradient streams across the South Central Plains of Arkansas. Eighteen sites were sampled for water chemistry, physical in-stream habitats, and macroinvertebrate assemblage structure. Multivariate statistics and correlations were used to analyze these variables. Land use had no measurable relationship with macroinvertebrate assemblages, likely because our study did not include streams with very high anthropogenic land use. There were significant correlations between water chemistry (driven primarily by total nitrogen, specific conductivity, and dissolved oxygen) and macroinvertebrate assemblage diversity. Macroinvertebrate assemblages varied across sites but were primarily grouped by river catchment, showing the strongest associations with dissolved oxygen, large woody debris, pool habitat, and discharge. Sub-habitat sampling demonstrated that root wads, woody debris, and riffles had the highest abundances and taxonomic richness, while soft sediments had the lowest percent Ephemeroptera, Plecoptera, and Trichoptera. In summary, in-stream habitat and water chemistry showed stronger relations to macroinvertebrate assemblages than land use, which aids the prioritization of monitoring of anthropogenic impacts across low-gradient streams.