The effects of freshwater input on water column light and aquatic primary productivity was measured in situ. Maps of turbidity and fluorescence in May, July and August of 1997 showed that two areas of high freshwater input significantly differed in both phytoplankton concentration and water column productivity. The Terrapin Bay complex in the western part of the study area was 40-200% higher in chlorophyll than in Little Madeira Bay to the east. Regions with highest surface chlorophyll levels in Terrapin Bay coincided with areas of high turbidity, indicating that much of attenuation of light in the water column may be biogenic, due primarily to phytoplankton blooms. In contrast, the spatial relationship between chlorophyll and turbidity in Little Madeira was mixed. Some areas of high turbidity coincided with low chlorophyll fluorescence while in other areas a direct correlation between turbidity and chlorophyll was indicated. In particular, in the region of greatest point-source freshwater input to Little Madeira at Taylor River mouth, fluorescence was elevated in areas low in turbidity, possibly indicative of enhanced phytoplankton productivity due to increased water clarity in freshwater inputs. The possibility that DOM or phytoplankton was imported to the area along with the freshwater flow remains to be determined. During development of the freshwater pulse in Little Madeira through August 1997, the region of highest transparency coincided with the region of lowest salinity, generally in the western half of the Bay, which was the prevailing direction of the plume. The marine-influenced areas in eastern and southern Little Madeira Bay, away from the plume, were more turbid, with high levels of suspended carbonate material. Downwelling attenuation coefficients (Kd) calculated from turbidity mapping data in August indicated that the area around Taylor River mouth had highest water transparency in Little Madeira Bay (and highest of all sub-basins in this study in northeastern Florida Bay), averaging about 1.5 m-1. This corresponds to about 35% of surface PAR reaching the bottom of the 0.70 m water column. Western Little Madeira Bay was similarly clear within the areas influenced by the fresh plume, where 22% of surface light reached the bottom of the 1.0 m water column, while the eastern bay average Kd of 2.5 suggests that less than 3% of surface PAR reached bottom of the 1.5 m water column. Terrapin Bay was equally low in transparency (Kd 2.4 m-1), but due to shallower water depths (z= 0.75 m), on average 16% of surface PAR reached bottom during the study period in August 1997.

The impact of a heterogeneous underwater light field on Thalassia productivity was assessed at paired stations in clear western and turbid eastern waters of Little Madeira Bay in August 1997. Changes in dissolved oxygen were measured in triplicate tip and base leaf sections of plants harvested from clear and turbid sites after incubation in BOD bottles under natural light. Plants from the clear sites, representing the area of the western bay influenced by the fresh water plume, showed evidence of adaptation to high light levels, exhibiting maximum photosynthetic rates (Pmax) from 70-300% higher than corresponding leaf sections in eastern bay plants. Mean productivity was 33 mg O2 g C h-1 for western plant specimens versus 15 for plants taken from eastern Little Madeira Bay. A simple modeling analysis performed using photosynthetic parameters from plant incubations and measured in situ light fields shows that average mid-day light levels in eastern Little Madeira Bay during August wet season measurements were below the compensation level for Thalassia. In contrast, plants in the western part of Little Madeira Bay were well above compensation light levels during the same period. As indicated by turbidity maps from transects made throughout the rainy season, water column transparency in Little Madeira Bay was heterogeneous, and tended to decline in areas dominated by marine water masses. Wind mixing events and marine intrusions are the most probable mechanisms for sporadically increasing local turbidity, which could negatively influence Thalassia productivity by imposing periods of light limitation. It is likely that rooted plants in the western part of Little Madeira Bay on average receive higher light levels, exhibit higher productivity rates, and can likely maintain net positive production during short episodes of low water clarity, than plants in the eastern and southern areas of the bay.