The latest research in WSNs (Wireless Sensor Network) has been exploring Underwater Acoustic Sensor Networks (UASNs). As the name suggests, these networks aim at providing effective communication underwater by addressing the challenges prevalent in this network. Underwater communication has found a lot of applications in ocean monitoring and underwater contamination monitoring. The issue of routing underwater is a major concern as it has to address a lot of challenges. Creating an effective routing protocol has been a constant topic of research in UASNs. We have focused on a Secure Cross-Layer Routing Protocol (SCLRP) in UASNs using Fuzzy Logic and Enhanced Algebra Homomorphic Encryption. This protocol aims at providing secure data transmission using optimized nodes that are selected from the neighboring nodes of the source node. The optimal nodes are selected by applying fuzzy rules to the available input. The selected nodes will then forward the packets to the next hop till the packet reaches the destination. The proposed protocol is an Energy Efficient Secure Fuzzy Logic based Cross –Layer design routing protocol. Our proposed protocol ensures safe transmission of data, which is the main objective of a routing protocol used in a wireless network. The routing protocol will ensure better QoS, by using a reliable encryption technique to reinforce secure routing. The protocol incorporates an enhanced Algebra Homomorphic encryption technique to help with managing the security of the transmitted data. QoS is further improved by using a cross-layer design wherein, the proposed protocol will not be expected to adjust as the data travels the different layers of the network so the protocol will be free from the confines of the standards and protocols followed in each of the layer. This flexibility will help in making our protocol perform better than the existing techniques. The SCLRP protocol is analyzed with the performance of NADIR and EEMCCP schemes to analyze its performance.