Water pollution by dyes is a serious environmental issue of modern society that needs to be addressed effectively. Herein, a promising adsorbent, i.e., 3D composite aerogel, was developed by using reduced graphene oxide and silk fibroin (rGO-SF) via hydrothermal and freeze-drying techniques. The efficiency of the prepared aerogel toward methylene blue (MB) dye adsorption was explored in batch adsorption experiments. A study revealed the adsorption capacity of rGO-SF120 as 249.89 mg/g toward methylene blue (MB) dye. The aerogel also selectively adsorbs MB over other dyes, such as rhodamine B (RhB) and methylene orange (MO). The adsorption process was mainly chemical (as data fitted well to both pseudo-second-order and Elovich kinetic models) and followed the Langmuir model, indicating that it formed a single layer of dye on its surface. Overall, the rGO-SF120 aerogel is an effective and potential candidate for treating dye-loaded water with high efficiency.