Selenate removal in drinking water is being vigorously debated due to the various health issues concerned. As a viable treatment option, this study investigated a fixed-bed biofilm reactor (FBBR) with internal recycling. The experimental design tested how hydraulic loading rate and electron donor affect selenate reduction together with other oxyanions. The tested accompanying oxyanions were nitrate and perchlorate and experiments were designed to test how an FBBR responded to the limited electron donor condition. The results showed that the reactor achieved almost complete selenate reduction with the initial hydraulic loading rate of 12 m3/m2/day (influent concentration of 1416 µg SeO42−/L). Increasing the hydraulic loading rates to 16.24 and 48 m3/m2/day led to a gradual decline in selenate removal efficiency. A sufficient external carbon source (C:N of 3.3:1) achieved an almost complete reduction of nitrate as well as selenate. The FBBR acclimated to selenate instantaneously and reduced nitrate via synergistic denitrification. An experiment with another oxyanion addition, perchlorate (459 µg ClO4−/L), revealed that perchlorate-reducing bacteria were more strongly associated with carbon limitation than selenate-reducing bacteria, which can help us to understand parallel reactions in FBBRs. This research provides a framework to further study the use of electron donor-controlled FBBRs for simultaneous reduction of selenate and other oxyanions threatening the drinking water-related environment and public health.