Wastewater-based epidemiology provides an approach for assessing the prevalence of COVID-19 in a sewer service area. In this study, SARS-CoV-2 RNA was measured in 44 wastewater-treatment plants of varying sizes that sampled approximately 67% of the population of Minnesota, from September 2020 through December 2022. Various linear regression models were investigated to predict the weekly case count from SARS-CoV-2 RNA concentrations under various transformation and normalization methods which we validated via cross-validation averaged across all treatment plants. We find that the relationship between COVID-19 incidence and SARS-CoV-2 RNA in wastewater may be treatment plant-specific. We study storage and time-to-analysis for RNA wastewater data and find large effects of storage temperature, indicating that collection methods may have an important effect on the utility and validity of wastewater data for infectious disease monitoring. Our findings are important for any large-scale wastewater surveillance program.