Samples are collected to measure nutrient and SS concentrations during various flows. For Group A sites, two samples are collected per month: one near the twelfth of the month and one during monthly base flow conditions. Additionally, at least four high flow events are sampled, targeting one per season. When possible, a second high flow event is sampled in accordance with spring planting in the basin. During high flow sampling events, samples are collected daily during the rise and fall of the hydrograph. The goal is to gather a minimum of three samples on the rise and three samples on the fall, with one sample as close to peak flow as possible. Sampling continues until flows returned to pre-storm levels.

For Group B sites, fixed date monthly samples are collected during the middle of each month. All samples are collected by hand with USGS depth integrating samplers. Samples are collected using the same protocol as Group A sites. At each site between 3- and 10-depth integrated verticals are collected across the water column and then composited to obtain a representative sample of the entire waterbody.

Whole water samples are collected to be analyzed for TN species, TP species, TOC, and SS. For Group B sites, SS samples are only collected during storm events. Additionally, filtered samples are collected to analyze for dissolved nitrogen (DN) and dissolved phosphorus (DP) species. All Pennsylvania samples are delivered to the PADEP Laboratory in Harrisburg to be analyzed the following workday. New York samples are sent to Columbia Analytical Services in Rochester, N.Y., for analysis the following workday. SS concentrations for Group A sites are completed at SRBC and for Group B sites at the USGS sediment laboratory in Kentucky. The parameters and laboratory methods used are listed below.