Sharpnose Shiner (Notropis oxyrhynchus) and Smalleye Shiner (N. buccula) are Brazos River endemics that have undergone range contractions and were federally listed as endangered in 2014, motivating an urgent need for robust, long-term monitoring that can track populations, habitat associations, and responses to changing flow and other stressors. Here, we detail a multi-year project that integrates standardized traditional fish sampling with novel, DNA-based approaches, including environmental DNA (eDNA) metabarcoding and the use of loop-mediated amplification (LAMP) assays to (1) optimize survey design for these focal minnows and their co-occurring fish assemblages, (2) support data-driven recommendations to agencies and stakeholders, and (3) develop transferable field and analytical tools (e.g., occupancy-detection modeling frameworks) that can be adopted for long-term, repeatable monitoring. We present project highlights with an emphasis on what we are learning by pairing capture-based surveys with genomics-enabled detection. Specifically, we synthesize emerging insights from (i) cross-method comparisons of taxonomic richness and community recovery, (ii) spatial and temporal patterns in fish assemblage composition across sites and seasons, as well as the environmental drivers of these patterns, and (iii) the degree of concordance (and mismatch) between traditional sampling and eDNA-based approaches for monitoring focal endangered shiners. Collectively, these findings reinforce the value of an integrated monitoring strategy: genomics tools, like eDNA metabarcoding, add sensitive, non-invasive, repeatable, community-level detection that strengthens occupancy inference and can complement and, in some cases, improve upon capture methods—especially for endangered species where handling risk, low density, and imperfect detection complicate conventional monitoring.