The major goal of this dissertation is to enhance software security by provably correct enforcement of in-depth policies. In-depth security policies allude to heterogeneous specification of security strategies that are required to be followed before and after sensitive operations. Prospective security is the enforcement of security, or detection of security violations before the execution of sensitive operations, e.g., in authorization, authentication and information flow. Retrospective security refers to security checks after the execution of sensitive operations, which is accomplished through accountability and deterrence. Retrospective security frameworks are built upon auditing in order to provide sufficient evidence to hold users accountable for their actions and potentially support other remediation actions. Correctness and efficiency of audit logs play significant roles in reaching the accountability goals that are required by retrospective, and consequently, in-depth security policies. This dissertation addresses correct audit logging in a formal framework. Leveraging retrospective controls beside the existing prospective measures enhances security in numerous applications. This dissertation focuses on two major application spaces for in-depth enforcement. The first is to enhance prospective security through surveillance and accountability. For example, authorization mechanisms could be improved by guaranteed retrospective checks in environments where there is a high cost of access denial, e.g., healthcare systems. The second application space is the amelioration of potentially flawed prospective measures through retrospective checks. For instance, erroneous implementations of input sanitization methods expose vulnerabilities in taint analysis tools that enforce direct flow of data integrity policies. In this regard, we propose an in-depth enforcement framework to mitigate such problems. We also propose a general semantic notion of explicit flow of information integrity in a high-level language with sanitization. This dissertation studies the ways by which prospective and retrospective security could be enforced uniformly in a provably correct manner to handle security challenges in legacy systems. Provable correctness of our results relies on the formal Programming Languages-based approach that we have taken in order to provide software security assurance. Moreover, this dissertation includes the implementation of such in-depth enforcement mechanisms for a medical records web application.