Modern money-laundering crimes involving professional money launderers and sophisticated dispersion techniques render it extremely difficult for investigative agencies to trace criminal proceeds. In particular, the problem of “commingled funds,” where criminal proceeds are mixed with legitimate assets and third-party funds, destroys the legal identity of funds and creates structural gaps that cannot be resolved by existing tracking methodologies. This study analyzed the challenges of tracing commingled funds, constructed a theoretical framework by applying the principle of Article 258 of the Civil Act (commingling) to determine the scope of criminal confiscation and forfeiture, and systematized six tracking hypotheses applicable to investigative practice: similarity of amounts, volatility of balances, temporal proximity, regularity of transactions, counterparty relationship, and subjective intent of the offender. Through a comparative legal analysis of the United States, United Kingdom, and Germany, this study proposed a commingled fund-tracking manual suitable for Korea’s legal environment and examined the balance between warrant-based control and fundamental rights protection.