Agents operating in unstructured environments often produce negative side effects (NSE), which are difficult to identify at design time. While the agent can learn to mitigate the side effects from human feedback, such feedback is often expensive and the rate of learning is sensitive to the agents state representation. We examine how humans can assist an agent, beyond providing feedback, and exploit their broader scope of knowledge to mitigate the impacts of NSE. We formulate this problem as a human-agent team with decoupled objectives. The agent optimizes its assigned task, during which its actions may produce NSE. The human shapes the environment through minor reconfiguration actions so as to mitigate the impacts of the agents side effects, without affecting the agents ability to complete its assigned task. We present an algorithm to solve this problem and analyze its theoretical properties. Through experiments with human subjects, we assess the willingness of users to perform minor environment modifications to mitigate the impacts of NSE. Empirical evaluation of our approach shows that the proposed framework can successfully mitigate NSE, without affecting the agents ability to complete its assigned task.