Water quality surveys are conducted on a routine basis from May to October.  Typically, 12 to 16 surveys are performed in a given year.  Survey consist of whole water column profile measurements, depth of solar radiation penetration, secchi depth readings, and the collection of raw water samples for laboratory analysis.  Parameters such as phosphorus, nitrate/nitrite, total suspended solids, chlorophyll a, and ammonia are analyzed to determine the relative health of the waters. Trace contaminates are sampled bi-annually, with sediment sampling taking place every other year.

The depth at which a sample is collected is determined by total water column depth at each station.  All samples area obtained by a Van Dorn grab sampler.  Nine stations are sampled at a top (one meter below the surface) and bottom depth (one meter above the sediment) on lower Green Bay and the Fox River.  The identification numbers for the nine stations are: 5, 7, 13, 16, 22, 32, 41, 51, and 56.  Stations 47, 55, and 57 are composite stations; where water is collected from both the top and bottom meter of water and then composited.  Several of GBMSD stations are located in extremely shallow waters.  At stations 10, 12, 23, 25, and 26, samples are collected at a mid-water depth.

During a typical field season, two continuous monitors are deployed.  One monitor is positioned at the mouth of the Fox River and the second is located in Zone 2 of Green Bay, near Entrance Light House.  Each monitor is programmed to collect data every 15 minutes for an approximate duration of 12 weeks during the field sampling season.