Two side-by-side experimental sub-surface flow systems allowed direct comparison of wetland performance under batch and continuous-flow operation. One system consisted of microcosm "columns" operated in 20-day batch mode while the second consisted of continuous-flow "cells" operated at a five-day residence time. Both systems treated identical synthetic domestic wastewater for two years and then treated identical synthetic mine-impacted water for one year. Each system had replicates planted with Typha latifolia, Scirpus acutus and unplanted controls. Temperature was cycled annually between 4 to 24 degrees C. Results indicated that plant species, season, and mode of operation interacted strongly in controlling dynamics of COD, nitrogen species, phosphate, sulfate, and redox potentials. In batch-loaded columns, between-species differences in oxidation and COD removal were large in winter, during plant dormancy, but absent in summer; COD removal, sulfate concentration, and redox potentials were closely correlated, suggesting that variation in root-zone oxygenation due to seasonal plant growth patterns and temperature-dependent plant and microbial respiration may explain observed differences. In the continuous-flow cells, species and seasonal differences were minimal or non-existent, indicating that under continuous-flow operation plants either did not influence root zone oxidation or that this influence had no effect on wetland performance for COD and nutrient removal or sulfate reduction.