Minnesota promulgated lake eutrophication standards in 2008 and is currently developing river eutrophication criteria as a part of the U.S. Environmental Protection Agency (EPA) nation-wide effort to develop nutrient criteria for lakes, rivers, wetland and estuaries. Data from representative medium to large rivers has shown strong, reproducible relationships among total phosphorus (TP), sestonic chlorophyll-a (Chl-a), and biochemical oxygen demand (BOD5) (Heiskary and Markus 2001). Subsequent advancements established linkages among these variables, diurnal dissolved oxygen (DO) flux, and fish and invertebrate metrics (Heiskary 2008 and Heiskary et al. 2010). Relationships among these variables, combined with statistical analysis of biologically-based thresholds, resulted in draft criteria (Table 1a). The criteria were developed in a regional context that is somewhat similar to aggregated (EPA) Level III ecoregions. The draft criteria and technical documentation have undergone initial review by (EPA) Region V and (EPA) Headquarters. The Minnesota Pollution Control Agency (MPCA) is updating that work and reviewing the draft criteria based on comments received. As a part of the Lake Pepin Total Maximum Daily Load (TMDL), the MPCA proposed site specific criteria for Lake Pepin. This work was done in concert with Lake Pepin TMDL Science Advisory Panel (SAP). Members of the SAP, including the Minnesota Department of Natural Resources (MDNR), Wisconsin DNR (WDNR), Metropolitan Council Environmental Services (MCES) and others, provided review and comment on the proposed criteria. The criteria were developed based on long-term data collections, modeling conducted by Limno Tech Int. (LTI) and a variety of research in support of the Lake Pepin TMDL. As work on this complex system progressed it became evident to staff and the SAP that site specific criteria for Lake Pepin needed to be linked with criteria for the Mississippi River navigation pools and criteria for the major rivers that drive the water quality of Lake Pepin and the pools: Upper Mississippi, Minnesota, and St. Croix Rivers. Also, low flow summers (e.g. 2006) and dramatic reductions in TP loading from the MCES Metro Plant to Pool 2 provided further insights into this system. As a result, the SAP recommended the MPCA move forward with an analysis of data for this overall system with the intent of developing eutrophication criteria for the rivers, pools, and Lake Pepin. This report provides an analysis of data for the navigation pools and major tributaries based on available data from MCES and MDNR’s Long Term Resource Monitoring Program (LTRMP), complements previous analysis for Lake Pepin (Heiskary and Wasley 2010), and contributes to development of eutrophication criteria for the Upper Mississippi River navigational pools. Mississippi River navigation Pools 1-8 represent a “transitional” waterbody type between free flowing rivers and true reservoirs. Similar to rivers, water residence time is quite short in all pools, with the exception of Pool 4 (Lake Pepin). Navigation is a very important component of these pools and considerable effort has been expended to create and maintain a navigational channel, which conveys the majority of water through the pools. These channels are really a “deep” river that is a relatively poor area for algal growth as compared to other rivers and lakes. The rivers, pools, and Lake Pepin, exhibit varying relationships between TP and Chl-a. The Minnesota, Upper Mississippi, St. Croix Rivers, and Pool 1 produce more Chl-a per unit TP than do Pools 2, 3, and Lake Pepin and all rivers and pools produce more Chl-a during low flow as compared to high flow. Downstream Pools 5-8 exhibit highly variable relationships between TP and Chl-a because of the dominance of upstream TP and Chl-a loads and the overall biological and physical complexity of these pools. Though we are currently unable to establish the distinct linkages among aquatic life and nutrients in these pools, (as we can for rivers or lakes), recent fishery survey information for the pools and Lake Pepin indicates a diverse and relatively healthy assemblage of fish is present. The proposed criteria are designed to protect aquatic life in rivers and pools (Table 1b), while also protecting aquatic recreation in Lake Pepin and protecting downstream aquatic life uses in Pools 5-8. They are consistent with criteria for large rivers and Lake Pepin developed by Wisconsin. Proposed criteria consider linkages among rivers, pools, and Lake Pepin, downstream transport of TP and algae, TP and Chl-a relationships, and desire to minimize the frequency of nuisance blooms (Chl-a > 50 μg/L). Related considerations include LTI Upper Mississippi River –Lake Pepin mechanistic model projections for the Lake Pepin TMDL and existing upstream TMDLs (e.g. Minnesota River low DO and Lake St. Croix TMDLs). Based on data compiled for this report, for the Mississippi at Anoka and Minnesota River at Jordan, both sites are likely to be deemed impaired based on these criteria. Total Maximum Daily Loads for these rivers would provide the roadmap for needed upstream reductions. Meeting the criteria in these two rivers is expected to result in downstream pool and Lake Pepin criteria to be met also. Based on recent LTRMP data, lower Pools 5-8 are at or below the draft Chl-a criterion and would likely be deemed to meet aquatic recreational uses. All tributaries downstream of Lake Pepin will have 100 μg/L TP (75 μg/L for wadeable streams in Wisconsin) standards based on the promulgated Wisconsin standards and Minnesota’s proposed river nutrient standards. Phosphorus loads to Pools 5-8 will continue to be reduced as upstream nutrient TMDLs are implemented. These reductions will provide additional protection for the pools just as the reductions in watersheds upstream of Lake Pepin will protect the pools upstream of Lake Pepin. Based on conversations to date with Wisconsin, these draft criteria fit their vision for these shared border waters as well.