Interference represents one of the most common barriers for the wireless communications society to bring the fully connected world to life, where everybody and everything is connected at any time, aiming to support a wide range of services and applications with increasing demand in terms of data rate with a higher degree of reliability and security, while keeping an affordable overall system capacity, complexity, and latency. Essentially, interference clearly explains the primitive nature of the wireless communications systems, where there is always an unwanted physical signal that disrupts the communication link, occurring from the physical layer (PHY) architecture of transmission signal, its interaction with the wireless channel and transceiver architecture in particular. Therefore, in past wireless technologies, waveform design along with wireless channel impairments and handset architecture define the main sources of interference, leading to inter-symbol interference (ISI), inter-carrier interference (ICI) and co-channel interference (CCI) types. In this line, recent advances in wireless technologies have revealed unprecedented interference types including inter-numerology interference (INI), inter-antenna interference (IAI), inter-waveform interference (IWI), cross-link interference (CLI) and inter-Doppler interference (IDI), while additional unique interference types are expected in near future. Consequently, a broader view of the interference has become a crucial need in order to avoid and relax its impact towards beyond 5G radio access technologies. Despite the extensive research in the literature performed by academia and industry, to the best of the authors’ knowledge, there is no work that provides a comprehensive taxonomy framework of interference sources and types, and a review of management techniques from the perspective of the PHY layer. This work aims to fill this gap in the literature. With this notation, in this survey, we propose an intuitive, generic, and expandable framework that categorizes the interference sources and their corresponding management solutions. In particular, we split the interference sources into two main groups by taking into account the user of interest such as self-user-interference (SUI) and other-user-interference (OUI), which we further classify considering the user’s intention about the presence of interference named intentional SUI (I-SUI), unintentional SUI (U-SUI), intentional OUI (I-OUI), and unintentional OUI (U-OUI). In line with this, we offer a classification of the interference management techniques regarding the source of interference. Lastly, the survey presents open research perspectives for beyond 5G wireless systems and concluding remarks.