Mortalities of young-of-the-year (YOY) smallmouth bass (Micropterus dolomieu) recently have occurred in the Susquehanna River due to Flavobacterium columnare, a bacterium that typically infects stressed fish. Stress factors include but are not limited to elevated water temperature and low dissolved oxygen during times critical for survival and development of smallmouth bass (May 1 through July 31). The infections were first discovered in the Susquehanna River and major tributaries in the summer months of 2005 but also were prevalent in 2007.

The U.S. Geological Survey, Pennsylvania Fish and Boat Commission, Pennsylvania Department of Environmental Protection, and PPL Corporation worked together to monitor dissolved oxygen, water temperature, pH, and specific conductance on a continuous basis at seven locations from May through mid October 2008. In addition, nutrient concentrations, which may affect dissolved-oxygen concentrations, were measured once in water and streambed sediment at 25 locations.

Data from water-quality meters (sondes) deployed as pairs showed daily minimum dissolved-oxygen concentration at YOY smallmouth-bass microhabitats in the Susquehanna River at Clemson Island and the Juniata River at Howe Township Park were significantly lower (p-value < 0.0001) than nearby main-channel habitats. The average daily minimum dissolved-oxygen concentration during the critical period (May 1–July 31) was 1.1 mg/L lower in the Susquehanna River microhabitat and 0.3 mg/L lower in the Juniata River. Daily minimum dissolved-oxygen concentrations were lower than the applicable national criterion (5.0 mg/L) in microhabitat in the Susquehanna River at Clemson Island on 31 days (of 92 days in the critical period) compared to no days in the corresponding main-channel habitat. In the Juniata River, daily minimum dissolved-oxygen concentration in the microhabitat was lower than 5.0 mg/L on 20 days compared to only 5 days in the main-channel habitat. The maximum time periods that dissolved oxygen was less than 5.0 mg/L in microhabitats of the Susquehanna and Juniata Rivers were 8.5 and 5.5 hours, respectively. Dissolved-oxygen concentrations lower than the national criterion generally occurred during nighttime and early-morning hours between midnight and 0800. The lowest instantaneous dissolved-oxygen concentrations measured in microhabitats during the critical period were 3.3 mg/L for the Susquehanna River at Clemson Island (June 11, 2008) and 4.1 mg/L for the Juniata River at Howe Township Park (July 22, 2008).

Comparison of 2008 data to available continuous-monitoring data from 1974 to 1979 in the Susquehanna River at Harrisburg, Pa., indicates the critical period of 2008 had an average daily mean dissolved-oxygen concentration that was 1.1 mg/L lower (p-value < 0.0001) than in the 1970s and an average daily mean water temperature that was 0.8 °C warmer (p-value = 0.0056). Streamflow was not significantly different (p-value = 0.0952) between the two time periods indicating that it is not a likely explanation for the differences in water quality.

During the critical period in 2008, dissolved-oxygen concentrations were lower in the Susquehanna River at Harrisburg, Pa., than in the Delaware River at Trenton, N.J., or Allegheny River at Acmetonia near Pittsburgh, Pa. Daily minimum dissolved-oxygen concentrations were below the national criterion of 5.0 mg/L on 6 days during the critical period in the Susquehanna River at Harrisburg compared to no days in the Delaware River at Trenton and the Allegheny River at Acmetonia. Average daily mean water temperature in the Susquehanna River at Harrisburg was 1.8 °C warmer than in the Delaware River at Trenton and 3.4 °C warmer than in the Allegheny River at Acmetonia. These results indicate that any stress induced by dissolved oxygen or other environmental conditions is likely to be magnified by elevated temperature in the Susquehanna River at Harrisburg compared to the Delaware River at Trenton or the Allegheny River at Acmetonia.