Two transect studies were conducted on Saylorville Reservoir, and ten transect studies were conducted on Red Rock Reservoir over a fifteen-month period. Each study consisted of dividing the reservoir into five transverse sections (transects) and the collection of depth samples at five stations along each transect. Therefore, there were a total of five transects and twenty-five stations during each study. Depth samples were collected at each station beginning at half a meter from the surface. Depending on the surface elevation at the time, the total number of samples collected for each water quality parameter varied from 75 to 239;Several water quality parameters were sampled, but those that were analyzed in this dissertation include: ammonia, suspended solids, dissolved oxygen, temperature, total phosphate, and nitrite plus nitrate nitrogen. A three-way analysis of variance approach was used to analyze the data in an attempt to characterize the spatial distribution of parameter concentrations within each reservoir. The results showed that thermal and chemical stratification occurs at both reservoirs. Depth gradients were often significant, while transverse and longitudinal variations were not. Besides, there was no evidence of channelization in any of the reservoirs. In fact, when the reservoirs are not stratified, the concept of complete mixing can be applied to them without much error;Three methods of time series analysis were also used to analyze the series of weekly water quality data that were collected at several sampling stations over the past nineteen years. The results showed that the concentrations of most parameters have not been increasing in the Des Moines and Raccoon Rivers, despite the common belief to the contrary.