How we’re learning about the estuary

To test the fourth hypothesis, our team first needed to document which sea-run fish species were present in the Penobscot River estuary, what parts of the estuary each species used over time,  abundance levels of each species in various parts of the estuary, as well as when and where their predators were present in the estuary. To collect this information, we needed to design a monitoring project that would be feasible for long-term efforts and the size of the study area.

Determining methodology

Our team started with reviewing monitoring efforts in other estuaries across the United States, specifically looking at different methods and gear types. The information helped us develop a project designed to evaluate best methods for collecting baseline fish data in the Penobscot River Estuary. 

Monitoring methods would need to be affordable, practical, and repeatable, given the physical and geomorphological features of the estuary. The Penobscot River estuary stretches from head of tide near Bangor down to Rockland, as defined by NOAA. It’s too small for a larger NOAA boat, but too big to survey by canoe. Boat time can be prohibitively expensive, especially for long-term monitoring efforts; and the survey area, equipment, and the number of days on the water can all factor into the price of collecting data. We designed our 2010-2013 survey to determine which monitoring, gear, and effort would be practical for the scope and scale of this estuary and to make sure we could still collect data that addresses the prey buffer hypothesis.


Several surveying techniques are possible and hydroacoustics is preferable for our goals.  Our findings indicated that a scientific-grade SONAR (dual frequency, split-beam system) for hydroacoustics was best for creating baseline data and monitoring the Penobscot River Estuary long-term. Split beam systems can be used to measure fish density, which is the number of fish in the water column and their relative size. This protocol is easy to use repeatedly, allowing researchers to collect information about biomass (a term roughly equivalent to “weight” of all the animals in an area) and measure changes in distribution over space and time (further details are available in O’Malley 2017).

We chose the area from Stockton Springs to Bangor as our monitoring area, as this captured a wide swath of environmental conditions from the ocean to river and the area was also being monitored with other studies of fish movement. We followed a predefined transect that zig-zagged from waypoint to waypoint, covering the areas of the estuary over six meters (roughly 18 feet) deep encompassing three marine mammal haul-out areas and two known cormorant rookeries. In addition to measuring fish density (how many fish) and relative size, our team also measures temperature, salinity, turbidity, pH, dissolved oxygen, and takes a census of marine mammals and birds.

Additional findings are presented in Lipsky et al. 2019.

6 hypotheses to address low survival rates of Gulf of Maine Atlantic Salmon

  1. Climate change and variability have altered oceanic salmon habitat, affecting marine survival of Gulf of Maine Atlantic salmon;
  2. Altered oceanographic conditions have led to changes in migration routes/behavior, resulting in reduced marine survival of Gulf of Maine Atlantic salmon;
  3. Changes in Northeast Shelf marine communities have altered Atlantic salmon food webs, resulting in reduced marine survival of Gulf of Maine Atlantic salmon;
  4. Populations of other diadromous species in the Gulf of Maine have declined, resulting in reduced marine survival of Gulf of Maine Atlantic salmon;
  5. Climate change has disrupted the correspondence between freshwater and saltwater conditions, leading to greater mortality rates of smolts and affecting marine survival of Gulf of Maine Atlantic salmon; and
  6. A loss of genetic diversity has reduced life history diversity, including adult run timing and variability in marine migration routes, affecting marine survival of Gulf of Maine Atlantic salmon.