In the Sub-Saharan African region of the River Niger Basin, where none of the major rivers is fully contained within the borders of a single nation, riverine ecosystem health monitoring is essential for survival. Even the globally proclaimed goals of sustainability and environmental security in the region are unattainable without using geospatial technologies of remote sensing and Geographic Information Systems (GIS) as conduits for environmental health within shared waters. Yet the systematic study of the nature of cooperation between states over shared water resources in troubled areas of the Middle East continues to dominate the literature with minimal coverage of the Sub- Saharan Africa experience and the role of GIS and remote sensing in monitoring the problem. Considering the intense ecosystem stress inflicted on River Niger by human activities and natural forces emanating from upstream and downstream nations. Researching the growing potential for acute riverine ecosystem decline among the nations of Niger and Mali along the River Niger Basin with the latest advances in spatial information technology as a decision support tool not only helps in ecosystem recovery and the avoidance of conflicts, but it has the potentials to bring countries much closer through information exchange. While the nature of the problem remains compounded due to the depletion of available water resources and environmental resources within shared waters, the lack of information exchange extracts ecological costs from all players. This is essential as the Niger Basin nations move towards a multinational watershed management as a conduit for sustainability. To confront these problems, some research questions with relevance to the paper have been posed. The questions include, Have there been any declines in the riverine ecosystem of the study area? What are the effects and what factors trigger the changes? What mitigation measures are in place for dealing with the problems? The first objective of the paper is to develop a new framework for analyzing the health of riverine ecosystems while the second objective seeks a contribution to the literature. The third objective is to design a geo-spatial tool for riverine ecosystem management and impact analysis. The fourth objective is to measure the nature of change in riverine environments with the latest advances in geo-spatial information technologies and methods. In terms of methodology, the paper relies on primary data sources analyzed with descriptive statistics, GIS techniques and remote sensing. The sections in the paper consist of a review of the major environmental effects and factors associated with the problem as well as mitigation measures in Mali and Niger. The paper concludes with some recommendations. The results point to growing modification along the riverine environments of the Mali and Niger portions of the River Niger Basin due to a host of factors.