Growing populations and climate change along the coastal regions of the world are an increasing reason for concern. Human alterations and land-use change have the potential to influence the ecology of the coastal ocean. Here I examine a link, an estuarine-lagoon, between land and the coastal ocean in Monterey Bay, California. The results show that the discharge plume from the Elkhorn Slough estuary represents a significant link between land and coastal ocean. The discharge plume extends ~1 km offshore in a south-westerly direction and is less than 1 km wide. The discharge plume is a resolvable feature when compared against the background of ambient Monterey Bay coastal waters, during the rainy months of December and January. The discharge plume is associated with elevated concentrations of dissolved organic matter and nitrate. Particulate matter appears to settle quickly through the water column and is transported in a southwesterly direction with the littoral currents, while the finer sediments and dissolved organics are transported northward to a phytoplankton bloom incubation region. Fatty acid analysis of filtered water samples showed biologically distinct waters types between the Elkhorn Slough plume and the receiving waters of the coastal ocean. A remarkable feature of the biological content of the plume is the abundance of bacteria-specific fatty acids which correlate well with the concentrations of colored dissolved organic matter (CDOM). Results also showed that plume waters contained higher concentrations of diatoms and cryptophytes, while the coastal ocean waters showed higher relative concentrations of dinoflagellates. Bacteria and cryptophytes can serve as nutrition for mixotrophic species of dinoflagellates. Lastly, using three different algorithms from the Moderate Resolution Imaging Spectrometer, I describe the seasonal and inter-annual spatial patterns of phytoplankton abundance within Monterey Bay. Statistically, all three algorithms performed equally well compared with in situ chlorophyll concentrations, but they describe different spatial patterns of phytoplankton abundance. The patterns described by the fluorescence line height (FLH) algorithm, which measures the natural fluorescence of phytoplankton, appear to coincide more closely with previously described oceanographic bloom phenomena. Spatial patterns of using the FLH algorithm also show higher concentrations of phytoplankton in the vicinity of the landbased nutrient sources from Elkhorn Slough discharge.