The Mississippi River is one of the world's 10 largest rivers, with average freshwater discharge into the northern Gulf of Mexico (GOM) of 380km(3) year(-1). In the northern GOM, anthropogenic nitrogen is primarily derived from agricultural fertilizer and delivered via the Mississippi River. The general consensus is that hypoxia in the northern Gulf of Mexico is caused primarily by algal production stimulated by excess nitrogen delivered from the Mississippi-Atchafalaya River Basin and seasonal vertical stratification of incoming stream flow and Gulf waters, which restricts replenishment of oxygen from the atmosphere. In this paper, we review the controversial aspects of the largely nutrient-centric view of the hypoxic region, and introduce the role of non-riverine organic matter inputs as other oxygen-consuming mechanisms. Similarly, we discuss non-nutrient physically-controlled impacts of freshwater stratification as an alternative mechanism for controlling in part, the seasonality of hypoxia. We then explore why hypoxia in this dynamic river-dominated margin (RiOMar) is not comparable to many of the other traditional estuarine systems (e.g., Chesapeake Bay, Baltic Sea, and Long Island Sound). The presence of mobile muds and the proximity of the Mississippi Canyon are discussed as possible reasons for the amelioration of hypoxia (e.g., healthy fisheries) in this region. The most recent prediction of hypoxia area for 2009, using the current nutrient-centric models, failed due to the limited scope of these simple models and the complexity of this system. Predictive models should not be the main driver for management decisions. We postulate that a better management plan for this region can only be reached through a more comprehensive understanding of this RiOMar system-not just more information on river fluxes (e.g., nutrients) and coastal hypoxia monitoring programs.