Establishing and maintaining safe, sufficient and effective Environmental Health (EH) conditions in health care facilities (HCFs), largely through water, sanitation and hygiene interventions, is critical to preventing and controlling infections and disseminating environmental health education. Malawi has recently drafted an EH policy with specific targets for HCFs, but there has been incomplete and unequal implementation of the policy. This study assesses the shortcomings and successes of implementing this and other EH related policies in Malawi’s HCFs. Through 53 interviews with EH officials from Malawi’s Ministry of Health, with representatives from the national to community level, we evaluate the implementation of these policies using Contextual Interaction Theory (CIT). Identified barriers include: limited political and financial support for and prioritization of the EH department; inadequate community mobilization; insufficient knowledge of policies and training of EH officials; staffing gaps in the EH working system leading to incomplete of reporting and supervision; and poor coordination with external actors leading to inefficient use of external resources to address existing service gaps. Respondents offered several solutions to these barriers, from which we propose several recommendations to improve the implementation process. Further research is needed to consider the cost-effectiveness and feasibility of these solutions to strengthen the implementation process within Malawi and elsewhere.