Evaluating water quality and the health of aquatic organisms is challenging in systems with systematic diel (24 hour) or less predictable runoff-induced changes in water composition. To advance our understanding of how to evaluate environmental health in these dynamic systems, field studies of diel cycling were conducted in two streams (Silver Bow Creek and High Ore Creek) affected by historical mining activities in southwestern Montana. A combination of sampling and modeling tools were used to assess the toxicity of metals in these systems. Diffusive Gradients in Thin Films (DGT) samplers were deployed at multiple time intervals during diel sampling to confirm that DGT integrates time-varying concentrations of dissolved metals. Thermodynamic speciation calculations using site specific water compositions, including time-integrated dissolved metal concentrations determined from DGT, and a competitive, multiple-metal biotic ligand model incorporated into the Windemere Humic Aqueous Model Version 6.0 (WHAM VI) were used to determine the chemical speciation of dissolved metals and biotic ligands. The model results were combined with previously collected toxicity data on cutthroat trout to derive a relationship that predicts the relative survivability of these fish at a given site. This integrative approach may prove useful for assessing water quality and toxicity of metals to aquatic organisms in dynamic systems and evaluating whether potential changes in environmental health of aquatic systems are due to anthropogenic activities or natural variability.