Background: The recent approval of agents from novel therapeutic classes including immunotherapy and antibody-drug conjugates has transformed the treatment landscape of advanced bladder cancer. However, even among patients with initially favorable responses to therapy, a subset of patients develop acquired resistance for reasons that are yet to be fully elucidated. Methods: To gain insight into the dynamics of tumor evolution during the course of treatment, we performed longitudinal profiling of plasma cell-free DNA in a cohort of 71 patients with muscle-invasive or advanced disease before, during, and/or after specific lines of therapy. To further resolve evolutionary dynamics during the course of treatment, we additionally performed Whole Exome Sequencing (WES) on 47 plasma samples across 25 patients. Results: We observed a median tumor purity of 3.8% in the plasma with a range from undetectable (N = 24 samples out of 217 total) to 61%, with tumor purity generally increasing in patients with progressing disease as compared to stable (p = 0.037) or to responding disease (p = 0.002), consistent with the notion that tumor DNA content in the circulation may act as a proxy for overall tumor burden. Phylogenetic reconstruction in 14 patients using WES data identified growing subclones with potential resistance drivers including TP53, PTEN, and FAM46C. In addition, we identified two cases in which growing subclones showed few shared mutations with regressing clones, demonstrating instead largely distinct somatic mutation profiles. Conclusions: Longitudinal WES of cfDNA is feasible in a subset of advanced bladder cancer patients with sufficiently high tumor purity in the blood. In addition, based on our findings of substantial variation in somatic mutations within two reconstructed patient phylogenies, we hypothesize that acquired resistance could in some cases be enabled by marked transitions in the neoantigen repertoire.