Aquatic macroinvertebrates inhabit virtually all freshwater ecosystems, yet communities in extreme saline environments remain largely undescribed, particularly in the Tropical Andes. This study characterizes the taxonomic diversity of aquatic macroinvertebrates in a travertine-fed saline stream (salinity: 12.5 ± 0.2 g/L; 2520 m a.s.l., southern Ecuador) and compares it with an adjacent freshwater stream. Macroinvertebrates were sampled on four occasions (n = 4 events per stream) using a multi-habitat D-net technique; physicochemical variables were compared with Mann–Whitney U exact tests, and diversity metrics with exact permutation tests (C(8,4) = 70 permutations) supplemented with Cliff’s delta as effect-size estimator. Community composition was assessed with ANOSIM and non-metric multidimensional scaling (NMDS). A total of 919 individuals were collected. The freshwater stream harbored significantly greater richness (49 genera, 28 families), abundance, and Shannon diversity than the saline stream (14 genera, 8 families; all p = 0.029, Cliff’s δ = 1.00), while Pielou’s evenness did not differ between stream types. Community composition was fully separated (ANOSIM R = 1.00, p = 0.028), with salinity (R² = 0.95, p < 0.01) and water temperature (R² = 0.79, p = 0.03) as the primary environmental drivers. The saline stream was dominated by halotolerant Diptera (Ceratopogonidae, Stratiomyidae) and water mites (Hydrachnidae), with virtually no EPT (Ephemeroptera–Plecoptera–Trichoptera) representation. These findings establish the first macroinvertebrate diversity baseline for a travertine-associated saline stream in the Tropical Andes, highlighting salinity and temperature as key environmental filters of aquatic biodiversity in extreme Andean lotic ecosystems.