The Heron Lake System historically has been an important resource for waterfowl in Southern Minnesota, USA. In the early 1900s, the system was a major nesting, feeding, and staging area for breeding and migrating waterfowl mainly due to the extensive growth of sago pondweed, Stuckenia pectinata. In recent years, the abundance of S. pectinata has decreased dramatically. We conducted a study from 2002 through 2003 to identify factors limiting the success of S. pectinata. Distribution and biomass of S. pectinata differed significantly over the years of this study. Biomass was related to environmental factors, including water transparency and water temperature early in the season. Water transparency during May (time of early growth) had a negative relationship with maximum biomass at each site over all years. Water temperature had a positive relationship with increases in seasonal biomass yield of S. pectinata in the Heron Lake System.