State trace analyses assess the latent dimensionality of a cognitive process by asking whether the means of two dependent variables conform to a monotonic function across a set of conditions. Using an assumption of independence between the measures, recently proposed statistical tests address bivariate measurement error, allowing both frequentist and Bayesian analyses of monotonicity (e.g., Davis-Stober, Morey, Gretton, & Heathcote, 2016; Kalish, Dunn, Burdakov, & Sysoev, 2016). However, statistical inference can be biased by unacknowledged dependencies between measures, particularly when the data are insufficient to overwhelm an incorrect prior assumption of independence. To address this limitation, we developed a hierarchical Bayesian model that explicitly models the separate roles of subject, item, and trial-level dependencies between two measures. Assessment of monotonicity is then performed by fitting separate models that do or do not allow a non-monotonic relation between the condition effects (i.e., same versus different rank orders). The Widely Applicable Information Criterion (WAIC) and Pseudo Bayesian Model Averaging – both cross validation measures of model fit – are used for model comparison, providing an inferential conclusion regarding the dimensionality of the latent psychological space. We validated this new state trace analysis technique using model recovery simulation studies, which assumed different ground truths regarding monotonicity and the direction/magnitude of the subject- and trial-level dependence. We also provide an example application of this new technique to a visual object learning study that compared performance on a visual retrieval task (forced choice part recognition) versus a verbal retrieval task (cued recall).