Biological assessment of the Minnesota River Basin was performed partly through the analysis of benthic macroinvertebrate communities. The study sites included mainstem, major and minor tributaries within the watershed. The communities were sampled using Hester-Dendy, kick-net and hand picking techniques. Once the community compositions were sorted they were analyzed using a series of metrics.

The MRAP fish study used the index of Biological Integrity (IBI) and habitat quality to assess the status of the Minnesota River Watershed's fish community and measure pollution impacts to the system. The first consideration the researchers needed to address was the establishment of biological criteria for the Minnesota River Basin. It was determined that an IBI score of 30 would be considered the criteria. 116 sites were then sampled using electrofishing techniques.

Level I of the MRAP land use study concentrated on the development of methodologies for evaluating nonpoint source pollution potential (NPSPP) in the major and minor watersheds that compose its basin. A model developed by the Minnesota Pollution control Agency was used for this task. 1,113 minor watersheds in the Minnesota River were tested and their results tabulated into weighted NPSPP and average NPSPP values for the 12 major watersheds of the Minnesota River. Cumulative values were also calculated to demonstrate the potential effects on the mainstem of the Minnesota River.

Level IV of the MRAP land use study is the methodology developed to use aerial photographs to determine land use and nonpoint source pollution within minor watersheds. These data were then to be transformed onto GIS maps. The type of photography used was color infrared aerial photography (CIR). The CIR pictures allow more accurate interpretation of land use type through greater definition. Through this process land use types that both contributed to and abated pollution were identified and mapped.