Tracking changes in stream nutrient inputs to Lake Erie over multidecadal time scales depends on the use of statistical methods that can remove the influence of year-to-year variability of streamflow but also explicitly consider the influence of long-term trends in streamflow. The methods introduced in this paper include an extended version of Weighted Regressions on Time, Discharge, and Season (WRTDS) modeling that explicitly considers nonstationary streamflow by incorporating information on changes in the frequency distribution of daily measured streamflow (discharge) over time. Soluble reactive phosphorus (SRP) trends in annual flow-normalized fluxes (loads) at five long-term monitoring sites in the western Lake Erie drainage basin show increases of 109 to 322% over the period 1995 to 2015. About one-third of the increase appears attributable to increasing discharge trends, while the remaining two-thirds appears to be driven by changes in concentration versus discharge relationships reflecting higher concentrations for any given discharge during recent years. Trends in total phosphorus and three nitrogen parameters (total nitrogen, nitrate-nitrite, and total Kjeldahl nitrogen) at the 10 sites analyzed were much less pronounced, and commonly show decreases in concentration-discharge relationships accompanied by increases in discharge, resulting in little net change in total flux. Trends in monthly SRP fluxes and discharge, dissolved versus particulate fractions of nutrients, and N:P flux ratios were also evaluated. The methods described here provide tools to more clearly discern the effectiveness of nutrient-control strategies and can serve as ongoing measures of progress, or lack of progress, towards nutrient-reduction goals.