We introduce a comprehensive approach to enhance the security, privacy, and sensing capabilities of integrated sensing and communications (ISAC) systems by leveraging random frequency agility (RFA) and random pulse repetition interval agility (RPA) techniques. The combination of these techniques, which we collectively refer to as random frequency and pulse repetition interval agility (RFPA), with channel reciprocity-based key generation (CRKG) obfuscates both Doppler frequency and pulse repetition intervals (PRIs), significantly hindering passive adversaries’ ability to estimate radar parameters. In addition, a hybrid information embedding method integrating amplitude shift keying (ASK), phase shift keying (PSK), index modu13 lation (IM), and spatial modulation (SM) is incorporated to significantly increase the system’s achievable bit rate. Next, a sparse-matched filter receiver design is proposed to efficiently decode the embedded information with a low bit error rate (BER). Finally, a novel RFPA-based secret generation scheme using CRKG enables secure code creation without a coordinating authority. The improved range and velocity estimation, and the reduced clutter effects achieved by the method, are demonstrated through the evaluation of the ambiguity function (AF) of the proposed waveforms.