Federal regulations for municipal separate storm sewer systems (MS4s) in the United States have been in place since 1990 as part of the Nation Pollutant Discharge Elimination System (NPDES), aiming to reduce sediment and pollutant loads originating from urban areas. However, small-municipality (Phase II) MS4s frequently grapple with several challenges, resulting in a lack of stakeholder buy-in and actionable stormwater management plans. We identify five common challenges concerning MS4 requirements based on literature review, professional experience, and feedback solicited from stakeholders, municipal managers, and fellow professionals and offer real-world examples of efficient, effective MS4 frameworks and/or solutions. The five challenges are summarized as beliefs that: (1) agricultural land use is the largest pollutant contributor and the root cause of pollution problems; (2) stormwater management only benefits downstream communities; (3) large, expensive projects are required to comply with regulations; (4) maintenance, monitoring, and inspection of best management practices (BMPs) is overwhelmingly complex and expensive; and (5) a lack of direct funding makes complying with regulations an impossible task. These challenges are universal in nature for Phase II MS4 permittees and can create real barriers for effective stormwater management. However, we found many examples of methods or techniques to effectively address these five specific challenges, making them well-suited and important for discussion. BMPs can create tangible improvements for surrounding communities (e.g., reduced streambank erosion and flooding), and improved understanding of the structure and options within the MS4 program will help small municipalities make informed choices about management plans.