During his early years at Allahabad University, Basu received the E. G. Hill Memorial Prize of the university in 1949 for the best research work by a member of the science faculty. The Indian National Science Academy elected Basu as a fellow in 1964 and the University of London honored him with the degree of Doctor of Science in 1965. The ensuing years would see him receive several honoris causa doctorates from Indian universities viz. Meerut University (1976), Kanpur University (1996), Jhansi University (2000) and Banares Hindu University (2000). The Council of Scientific and Industrial Research awarded him the Shanti Swarup Bhatnagar Prize, one of the highest Indian science awards, in 1965. The Federation of Indian Chambers of Commerce & Industry awarded him the FICCI Award for Science and Technology in 1975 and he received the Professor T. R. Seshadri Seventieth Birthday Commemoration Medal of the Indian National Science Academy in 1976 and the P. C. Ray Award of the Indian Chemical Society in 1977. He was awarded the National Fellowship by the University Grants Commission in 1980 and the Golden Jubilee Medal by the Institute of Science, Mumbai in 1984.
The J. C. Ghosh Medal of the Indian Chemical Society reached Mehrotra in 1986, followed by the Academic Achievements Award of the Sōka University in 1987. The Indian Science Congress Association honored him with four awards; starting with the Platinum Jubilee Distinguished Service Award in 1988; followed by G. P. Chatterjee Award  in 1991, Acharya Narendra Dev Award in 1992 and Ashutosh Mukherjee Award in 1993. In between, he received the inaugural Atmaram Award of the Central Institute of Hindi. The Chemical Research Society of India awarded him Lifetime Achievement Award in 1999 and the Indian Chemical Society awarded him the Platinum Jubilee Award in 2000. He was an elected fellow of the Indian Academy of Sciences, Indian National Science Academy and National Academy of Sciences, India and a fellow of the Chemical Society of London, Royal Institute of Chemistry and the Indian Chemical Society. He also delivered several award orations and featured lectures; Special lecture at the XVII International Conference on Coordination Chemistry (1977), Plenary lecture at the XIX International Conference on Coordination Chemistry (1978), Plenary lecture at the IV International Conference on Solute-Solvent Interaction (1978), Clarence Karcher Memorial Lecture of University of Oklahoma (1982), the inaugural Foundation Lecture of the Federation of Asian Chemical Societies (1987) and N. R. Dhar Memorial Award Lecture of the National Academy of Science, India (1991) are some of the notable ones.