Mobile ad hoc networks (MANETs) are wireless networks established by autonomous nodes without the aid of any established infrastructure. In MANETs, the nodes themselves implement the network management in a cooperative fashion and thus, all of them are responsible for this. Due to their wireless-mobile nature MANETs are susceptible to various attacks. This thesis focuses on exploring the attacks performed at the two most vulnerable layers, namely the Data Link and the Network layer. The ability to effectively detect these attacks is considered crucial for the survival of MANETs. Therefore, we provide a critical analysis of the most recently proposed detection schemes for both layers which can be used as bedrock for the creation of novel intrusion detection engines. In addition, this thesis proposes an Intrusion detection engine that is capable of detecting the majority of attacks performed at the MAC layer. The engine utilizes a specification-based mechanism, although it also uses some threshold based rules.