Ecological analyses of ancient marine communities are impacted by the environmental gradients controlling assemblage compositions and the heterogeneous distribution of shell material. Carbonate systems are also heterogeneous at small spatial scales, and microfacies analysis may highlight sources of environmental variation impacting ancient communities. Closely spaced, replicate sampling of fauna can mitigate the effects of heterogeneity and improve multivariate analyses, but this technique has rarely been combined with similar sampling of lithologic data. This study analyses lithological and faunal data to determine the environmental gradients controlling the composition of Mississippian fossil assemblages of the lower Madison Group in Montana. Eighty-one lithological and faunal samples were collected from four stratigraphic columns in Montana, which represent the deep-subtidal, foreshoal, and ooid-shoal depositional environments within one 3^rd-order depositional sequence. Lithologic samples were thin sectioned, and point counted to quantify lithologic compositions for each faunal sample. Color sedimentary structures, and bioturbation were also described for each lithological sample to provide additional environmental proxies. Cluster analysis identifies three distinct lithological associations across all depositional environments— crinoid-dominated carbonates, peloidal-crinoidal carbonates, and micritic-crinoidal carbonates. Cluster analysis and nonmetric multidimensional scaling identifies a highly diverse brachiopod biofacies and a solitary coral-dominated biofacies along an onshore–offshore gradient. Lithological data and ecologic characteristics indicate that substrate and wave energy potentially covary with the onshore–offshore gradient. Overlaying lithological information on the NMS indicates a secondary gradient reflecting oxygen that is expressed by increasing bioturbation and gradation from dark gray carbonates to medium-light gray carbonates. This study demonstrates how combining closely spaced, replicate sampling of faunal assemblages with lithologic samples details potential sources of lithological and ecological variation, enhances multivariate analyses, and allows for a greater understanding of environmental gradients.