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Due to the unpredictable nature of intense storms and logistical constraints of sampling during storms, little is known about their immediate and long-term impacts on water quality in adjacent aquatic ecosystems. By combining targeted experiments with routine monitoring, we evaluated immediate impacts of two successive storm events on water quality and phytoplankton community response in the tidal James River and compared these findings to a non-storm year. The James River is a subestuary of the Chesapeake Bay and sampling was conducted before, during, and after Hurricane Irene and Tropical Storm (TS) Lee in 2011 and during the same time period (late summer/early fall) in 2012 when there were no storms. We collected and compiled data on nutrient and chlorophyll a concentrations, phytoplankton abundance, nitrogen uptake, primary productivity rates, and surface salinity, temperature, and turbidity in the meso- and polyhaline segments of the James River. Hurricane Irene introduced significant amounts of freshwater over the entire James River and Chesapeake Bay watersheds, while rainfall from TS Lee fell primarily on the tidal fresh region of the James River and headwaters of the Chesapeake Bay. Dinoflagellates dominated the algal community in the meso- and polyhaline segments prior to the storms in 2011, and a mixed diatom community emerged after the storms. In the mesohaline river segment, cyanobacteria abundance increased after TS Lee when salinities were depressed, likely due to washout from the oligohaline and tidal fresh regions of the river. In 2012, dinoflagellates dominated the community in both segments of the river during late summer but diatoms were also abundant and their biomass fluctuated throughout the summer and fall. Cyanobacteria were not present in either segment. Overall, we observed that the high-intensity rainfall from Hurricane Irene combined with high flushing in the headwaters as a result of TS Lee likely reduced primary productivity and altered community composition in the mesohaline segment but not the more estuarine-influenced polyhaline segment. Understanding the influence of high freshwater flow with a short residence time associated with storms is key to the planning and management of estuarine restoration as such disturbances are projected to increase as a result of climate change.

Massive blooms of the harmful alga Cochlodinium polykrikoides Margalef occurred in the lower Chesapeake Bay and its tributaries during the summers of 2007 and 2008. The Lafayette and Elizabeth Rivers appeared to act as initiation grounds for these blooms during both years. However, in 2008 there were also localized sites of initiation and growth of populations within the mesohaline portion of the James River. Bloom initiation appeared to be correlated with intense, highly localized rainfall events during neap tides. Subsequent spring tides increased tidal flushing and transport of C. polykrikoides from the Lafayette and Elizabeth Rivers into the lower James River where it was transported upriver by local estuarine circulation. Blooms dissipated in response to increased wind-driven mixing associated with frontal systems moving through the region. A combination of physical factors including, seasonal rainfall patterns, increased stratification, nutrient loading, spring-neap tidal modulation, and complex estuarine mixing and circulation allowed C. polykrikoides to spread and form massive blooms over large portions of the tidal James River and the lower Chesapeake Bay.

During August and September 2007, the lower Chesapeake Bay and its tributaries experienced a massive bloom of Cochlodinium polykrikoides Margalef (>104 cells per milliliter) that persisted for over a month, was extremely patchy, and at times penetrated into the Atlantic Ocean. The onset of the bloom coincided with a period of intense rainfall and stormwater runoff after a protracted summer drought period. Genetic evidence showed this species to be distinct from many Asian strains but similar to other North American strains. Populations dominated by C. polykrikoides took up a variety of nitrogenous compounds to support their growth and were able to mobilize additional sources of organic nutrients through peptide hydrolysis. Bioassays determined that C. polykrikoides exerted a lethal affect on juvenile fish and shellfish, causing 100% mortality of juvenile fish (Cyprinodon variegates) in less than 24 h and 20% mortality in juvenile American oysters (~21 mm; Crassostrea virginica) within 72 h.

We developed an algorithm for calculating habitat suitability for seagrasses and related submerged aquatic vegetation (SAV) at coastal sites where monitoring data are available for five water quality variables that govern light availability at the leaf surface. We developed independent estimates of the minimum light required for SAV survival both as a percentage of surface light passing though the water column to the depth of SAV growth (PLW min) and as a percentage of light reaching reaching leaves through the epiphyte layer (PLL min). Value were computed by applying, as inputs to this algorithm, statistically dervived values for water quality variables that correspond to thresholds for SAV presence in Chesapeake Bay. These estimates ofPLW min andPLL min compared well with the values established from a literature review. Calcultations account for tidal range, and total light attenuation is partitioned into water column and epiphyte contributions. Water column attenuation is further partitioned into effects of chlorophylla (chla), total suspended solids (TSS) and other substances. We used this algorithm to predict potential SAV presence throughout the Bay where calculated light available at plant leaves exceededPLL min. Predictions closely matched results of aerial photographic monitoring surveys of SAV distribution. Correspondence between predictions and observations was particularly strong in the mesohaline and polythaline regions, which contain 75–80% of all potential SAV sites in this estuary. The method also allows for independent assessment of effects of physical and chemical factors other than light in limiting SAV growth and survival. Although this algorithm was developed with data from Chesapeake Bay, its general structure allows it to be calibrated and used as a quantitative tool for applying water quality data to define suitability of specific sites as habitats for SAV survival in diverse coastal environments worldwide.