A spectral amplitude coding optical code division multiple access (SAC-OCDMA) system has been utilized to compare its efficiency in free space and underwater using two different code families, such as the random diagonal (RD) code and the modified quadratic congruence (MQC) code. On account of a variety of ocean water properties, the efficiency of the RD code has been assessed for pure seawater and coastal water and collated with the performance of the MQC code. RD code’s performance has been compared with MQC to validate that the RD code is capable of providing improved performance in underwater channels. The bit error rate (BER) evaluation regarding underwater and free space has been integrated to discern which code family exhibits higher proficiency in which atmosphere for the proposed framework. Comparative inspection amid free space and underwater using common parameters such as transmitted power and number of simultaneous users has been conducted to verify the most suitable channel for the RD code.