Controlling nonpoint source pollution (NPSP) is very important for protecting the water environment, and surface-flow constructed wetlands (SFCWs) have been widely established to mitigate NPSP loads. In this study, the pollutant removal efficiencies, greenhouse gas (GHG) emissions, and chemical and microbial community properties of the sediment in a large-scale SFCW established beside a plateau lake (Qilu Lake) in southwestern China to treat agricultural runoff were evaluated over a year. The SFCW performed best in terms of nitrogen removal in autumn (average efficiency of 63.5% at influent concentrations of 9.3–35.4 mg L) and demonstrated comparable efficiency in other seasons (23.7–40.0%). The removal rates of total phosphorus (TP) and chemical oxygen demand (COD) were limited (18.6% and 12.4% at influent concentrations of 1.1 and 45.5 mg L on average, respectively). The SFCW was a hotspot of CH emissions, with an average flux of 31.6 mg m·h; moreover, CH emissions contributed the most to the global warming potential (GWP) of the SFCW. Higher CH and NO fluxes were detected in winter and in the front-end section of the SFCW with high pollutant concentrations, and plant presence increased CH emissions. Significant positive relationships between nutrient and heavy metal contents in the SFCW sediment were detected. The microbial community compositions were similar in autumn and winter, with Thiobacillus, Lysobacter, Acinetobacter and Pseudomonas dominating, and this distribution pattern was clearly distinct from those in spring and summer, with high proportions of Spirochaeta_2 and Denitratisoma. The microbial co-occurrence network in spring was more complex with stronger positive correlations than those in winter and autumn, while it was more stable in autumn with more keystone taxa. Optimization of the construction, operation and management of SFCWs treating NPSP in lake watersheds is necessary to promote their environmental benefits.