U.S. Department of Agriculture-Agriculture Research Service (ARS)
As one of the 14 Benchmark Watershed studies of the Conservation Effects Assessment Project (CEAP), ARS monitors eight stream sites (Appendices 1 and X) for discharge, nutrients, pesticides, and suspended sediment in the St. Joseph River Basin in northeast Indiana that will be used for process models nationally (fig. 3). All eight of these sites continue to be sampled in 2017 with three sampled since 2002, two since 2003, one since 2005, and two sites that have been moved but were sampled since 2002 and 2003, respectively. These sites include four edge of field and eight ditch/stream sites; only the eight ditch/stream sites are shown on the map. Field sites are sampled for nutrients, pesticides and suspended sediment, while ditch/stream sites are analyzed for nutrients and pesticides. Weather conditions and soil conditions are also monitored at 10 of these sites as well as four additional weather/soil moisture only sites.

United States Geological Survey (USGS)
The United States Geological Survey (USGS) has two long-term national monitoring networks designed to assess trends. The National Stream Quality Assessment Program (NASQAN) monitors large rivers and has two primary objectives which are to (1), address questions about the annual transport of selected constituents from selected large rivers to coastal waters of the United States and (2) address questions specific to the Mississippi-Atchafalaya River Basin related to hypoxia in the Gulf of Mexico. To accomplish this, all sites are co-located with USGS streamflow gages. NASQAN sites are sampled 14 times per year for nutrients, major ions, pesticides, suspended sediment, and dissolved organic carbon. Seasonal and annual loads of total and dissolved nutrients are determined from all the major subbasins within the Mississippi River Basin to the Gulf of Mexico to identify which sub-basins contribute the most nutrients. Because of the long period of record and colocation with streamflow gages, these sites allow for trend assessments. Annual loads and flow weighted concentrations are calculated and can be found at http://water.usgs.gov/nasqan/. There are four NASQAN sites that can be used to determine water quality conditions leaving the state of Indiana (fig 4).

The National Water Quality Assessment Program (NAWQA) has two sampling sites in Indiana; one site has been monitored since 1991–the White River at Hazleton (03374100)–and another site since 1993–Sugar Creek at New Palestine (394340085524601). These sites are sampled 20-26 times per year for nutrients, pesticides, suspended sediment, and selected major ions. Additionally, the Sugar Creek site is sampled for biological communities (algae, invertebrates, and fish) and habitat; Sugar Creek has been sampled for ecological communities 19 times since 1993. Sugar Creek is an indicator of agricultural influences and is one of 11 agricultural sites within the NAWQA national study design. The White River site is a large river site and reflects all the upstream inputs.

Furthermore, the USGS has five sites that are sampled in collaboration with state groups. All of these sites are also monitored continuously for different parameters and include sites in Eagle Creek, School Branch, and the Kankakee River (3 sites). These sites are not shown on this map but can be found in the section on continuous monitored sites (Appendices 1 and X).