<p>Microplastic contamination was assessed in a protected headwater catchment that supports the endangered Formosan landlocked salmon. Long-term water chemistry data (2013–2024) were summarized as pooled, station-level distributions, and microplastics were quantified during the 2024 dry season at seven monitoring stations, each with three technical replicates. Micro-Fourier transform infrared spectroscopy in reflection mode (4000–675 cm⁻¹ and 8 cm⁻¹ resolution) was applied using whole-filter mapping (step size 50 × 50μm) and strict spectral quality control. Particles were retained for enumeration only if they met a minimum library match threshold of 60% and showed clear visual confirmation of diagnostic absorption bands. The validated lower size limit for inclusion was ≥25 µm. Dry-season station means ranged from approximately 1.0 to 3.3 items L⁻¹. Principal component analysis (PCA) of standardized variables indicated that microplastic abundance was aligned with an ionic and nutrient gradient, which was characterized by conductivity, NO₃⁻–N, SO₄²⁻, PO₄³⁻, Cl⁻, and water temperature. A replicate-level negative binomial regression revealed a positive association between microplastic counts and the leading PCA axis representing this gradient. Polymer composition was dominated by the anthropogenic fiber rayon, with common plastics such as polyethylene terephthalate, polyethylene, and polypropylene also detected. These findings underscore the importance of source-targeted management strategies in protected streams, including riparian buffer zones and agricultural plastic controls in farming areas, as well as reduction of single-use items and improved wastewater treatment infrastructure in recreation-intensive zones.</p>