The presence of toxic substances such as persistent organic pollutants (POPs) in the environment, and in organisms including humans, is a serious public health and environmental problem, even at low levels and poses a challenging scientific problem. The Stockholm Convention on POPs (SC) entered into force in 2004 and is a large international effort under the United Nations Environment Programme (UNEP) to facilitate cooperation in monitoring, modeling and the design of effective and fair ways to deal with POPs globally. This paper is a contribution to the ongoing effectiveness evaluation (EE) work aimed at the assessment and enhancement of the effectiveness of the actions undertaken under the SC. First we consider some aspects related to the monitoring of POPs in the environment and then briefly review modeling frameworks that have been used to simulate long range transport (LRT) of POPs. In the final sections we describe the institutional arrangements providing the conditions for this work to unfold now and some suggestions for it in the future. A more effective use of existing monitoring data could be made if scientists who deposited them in publicly available and supervised sites were rewarded in academic and professional terms. We also suggest the development of multi-media, nested, Lagrangian models to improve the understanding of changes over time in the environment and individual organisms.