Rates of carbon storage in wetlands are determined by the balance of its inputs and losses, both of which are affected by environmental factors such as water temperature and depth. In the autumn of 1997, the U.S. Geological Survey re-established two wetlands with different shallow water depths—about 25 and 55 centimeters deep—to investigate the potential to reverse subsidence of delta islands by preserving and accumulating organic substrates derived from plant biomass inputs over time. Because cooler water temperatures can slow decomposition rates and increase accretion of plant biomass, water temperature was recorded from July 2005 to February 2008 in the deeper of the two wetlands, where areas of emergent and submerged vegetation persisted throughout the study, to assess differences in water temperature between the two vegetation types. Water temperature was compared at three depths in the water column between areas of emergent and submerged vegetation and between areas near the water inflow and in the wetland interior in both vegetation types. The latter comparison was a way of evaluating the effect of the length of time water had resided in the wetland on water temperatures.

There were statistically significant differences in water temperature at all depths between the two vegetation types. Overall, in areas of emergent marsh vegetation, the mean water temperature at the surface was 1.4 degrees Celsius (°C) less than it was in areas of submerged vegetation; however, when analyses accounted for the changes in temperature due to seasonal and diurnal cycles, differences in the mean water temperature between the vegetation types were even greater than this. For example, in the spring, the mean temperatures in areas of emergent marsh vegetation at the surface, mid-point, and near the sediment in the water column were 2.0, 2.3, and 2.1 °C less, respectively, than water temperatures in areas of submerged vegetation. When diurnal changes in temperature were accounted for by comparing temperatures in mid-afternoon (at 3 p.m.), water-temperature differences were even greater than the seasonal means indicated. In areas of emergent vegetation, the mean temperatures were cooler than temperatures in areas of submerged vegetation at the surface, the mid-point, and near the sediment in the water column by 3.9, 3.6, and 2.3 °C, respectively. Furthermore, from July 2005 through December 2006, water temperatures at the surface in the interior of the wetland were significantly cooler than in areas near the inflow supplying water from the San Joaquin River by 1.0 °C in areas of submerged vegetation and by 1.1 °C in areas of emergent vegetation.