Urbanization and human-led development have increased more rapidly along shorelines and in coastal watersheds than inland regions over the past century. The result of major land use changes for both urban tracts and agriculture to serve the urban areas, as well as infrastructure development is increased runoff carrying sediments, nutrients, pollutants, pharmaceuticals, and toxins downstream to estuarine systems. The increased runoff levels are only the tip of the iceberg, with human development resulting in increased fecal bacteria from urbanization and excess nutrients from agriculture leading to harmful algal blooms. Estuaries act as a natural filter between land and sea, but have been overloaded by the influx of sediments and pollutants in recent decades. As a result, there have been a variety of impacts to estuarine ecosystems and water quality including increased sediment load, eutrophication, harmful algal blooms, fecal bacteria, as well as shellfish and fisheries declines. In some estuarine systems, the reduction in light penetration to the benthos has led to the loss of seagrasses. In others, seasonal hypoxia is a visible symptom of prolonged eutrophication. There is a need to augment long-term monitoring techniques with new technologies and data processing methods to better understand the current state of estuaries and work towards mitigating human impacts on estuarine ecosystems and water quality.